cabbysaurus

Thanks for your response, I appreciate it. I agree with a lot of what you said and actually do not want to go into industry, so I guess that the location does not matter so much in those terms.
I think you're right that the professors at UW are trying to be honest and helpful. I'm not upset with them and actually appreciate their honesty  - I just wasn't aware of all of the different factors and implications at play. I am definitely worried about the potential competition for funding and labs, as you mentioned.
At this point, I am probably just letting my preference towards Seattle get in the way. Harvard is definitely a great program, the advisor is well-known and we get along well, plus I have the funding and actually feel wanted there. It seems silly to let location be the deciding factor. I guess I just needed to write this all out and see someone else's thoughts to come to that conclusion. So thank you! 

I'm the type of person who prefers having options and fallbacks, plus I love Berkeley, so would definitely choose that. It seems like you have more potential advisors and projects there. Were you able to chat with the students in PI 2's lab there?
My main concern about Berkeley would be the cost of living there, especially on a grad student stipend.

Are you set on researching protein NMR? Did the advisor at school 1 suggest other projects that you are interested in working on?
Also, what are you planning on doing over summers? If you're looking to do internships off campus, then maybe where you live for 9 months doesn't matter so much. Or maybe you make so much during your internship that you can live comfortably at school 2.
If all else fails, you can flip a coin, and when the coin is in the air you will know which way you want it to land and that's where you go. 
 

Northwestern requires only two letters. I think there are some smaller state schools that do as well.

I applied to PhD programs this year in a similar situation. I finished my undergraduate nearly 6 years ago and have been working since, first as a software engineer then as a CS teacher. I also completed a Master's in a related field (Computational Linguistics) part time.
I've been lucky enough to be admitted to a number of great universities (UW, Harvard, NYU to name a few) even despite a low undergraduate GPA. I don't say this to brag - just to let you know that it is certainly possible (as mentioned by @spamhaus as well). Here are the things I think helped my application greatly:
Research experience - this cannot be stressed enough. I did undergraduate research experience, a quarter worth of graduate research experience, and did a full research internship this past summer. None of this research resulted in publications, but by having done it I showed that I am invested in it and aware of what it entails. Letters - I got one letter from my undergrad research advisor and one from a professor who supervised me this summer. The third letter was from my old manager at Microsoft. I would recommend getting one letter from an employer, but the other two should definitely be from academia and the more well-known the better (as long as they're good of course). The letter from an employer should preferably be someone who has a graduate degree and thus can attest to your abilities to do research. They can also mention how great it is to work with you. Statement of purpose - I spent SO much time on this. The key was making it unique, showing my passion, and linking all of my past experiences (work, research, and teaching) to my desire for getting a PhD and success in getting it. GRE - I did at least average to all of the schools I applied to. Definitely study for it, especially having been out of school for a while. The math is not hard, but the way they ask the questions can be, so going through a lot of practice teaches you the tricks. Also take a lot of practice exams. Sitting for 5 hours straight is hard and I would not have made it had I not done a number of practice tests before hand. Now to answer your questions:
I think you really need to try and get research experience. This could be a long-distance project with a professor as @spamhaus mentioned, a summer opportunity as I did, or maybe even something at your job if possible. Without research experience, I don't think you will be a competitive candidate. I also think that you need to be prepared to quit your job in order to gain research experience if necessary.  For letters, you really need to get at least two people who can talk about your research. Those people should be professors or researchers with PhDs themselves. I think at least one of them should be recent (within the past year from your application). For where to apply, that depends on a lot of things like where you can relocate to, if they have things you're interested in researching, size of the program you want, etc. Some less competitive schools you could consider are Boulder and Northwestern. The most important thing is to find professors who have research that is aligned with yours, then to mention them in your SOP and say why their research interests you and how it aligns with your goals. As for getting another Master's, I think that could be definitely be helpful for getting better LORs and some research experience. However, you then have to think about how you would balance that with work and how you would pay for it. I think you may be better off looking for other research opportunities instead. I hope that helps! Of course, I'm not an admissions expert, just sharing my experience. Please feel free to reach out with additional questions.

Originally, when writing about prestige of a fellowship, I was thinking about the external fellowships, not University-internal ones. I don't think there is any large gain in prestige from a university-granted fellowship, unless it's something that comes from a University-wide competition and is well publicized, but even then, the level of prestige is not much to an external reader of your CV (however, as I wrote above, it can help your reputation within your department!)
I wouldn't pick a fellowship over a TA/RA just because of the prestige though. I don't think it makes a huge difference. However, I would certainly consider a slightly lower ranked school with a fellowship that means I don't have to do any TA or RA work and can focus on my dissertation over a slightly higher ranked school that required a large TA/RA work load. I would choose the funding package and school/advisor/research fit combination that would allow me to be the most productive!

In regards to fellowships being more prestigious - does that mean that going to a lesser ranked school (in terms of department reputation) with a fellowship would be comparable, or at least worth considering, vs. a higher ranked school with an assistantship?
I know that I can apply for external fellowships in the future, but had one good school offer me a 5 year fellowship... I'm wondering if this is something I should seriously consider over going to a top 10 school in my field where I will have to be a TA/RA, at least for a year or two.

Since you are Cellular and Molecular Biology, I think this response I wrote on the Biology forum will help:
A couple additional answers to your questions from my own experience as an interviewee and interviewer:
1. You don't have to prepare incredibly compelling questions for graduate students and faculty, just having anything is a positive in their eyes. But if you want to get a good glimpse into what they think, there are a few questions you should try to ask if appropriate.
For graduate students, you should ask about:
Their thoughts - both positive AND negative - on the program (such as the BBS program), institution (such as Harvard), and the city (such as Cambridge/Boston) What they do outside of science/lab What opportunities are available to graduate students - this includes teaching, internships, non-traditional paths, etc. What a typical day in lab is like for them - this will vary student to student and lab to lab, but can be revealing about the culture at an institution If there is anything else they wished they had known before starting graduate school (in general or in that specific PhD program) For faculty, you should ask about:
What they believe the greatest strengths and weaknesses are of the institution The research environment at the institution - especially in regards to collaboration (a lot of PIs love to talk to about how collaborative they are/their university is) Specific questions about their research (if you have any) Their expectations for a graduate student/what an ideal graduate student is to them If there is anything that they can talk about other than the research that makes the program/institution unique. If you look at graduate school interview prep websites, there will be a lot of "recommended" questions that include asking about graduation outcomes, fellowships, time to graduation, publishing, etc. It is okay to ask questions such as these, but a lot of this information will be covered in the introduction/orientation each program gives. In my opinion, you are better suited to ask questions such as those listed above.
2. The most basic biomedical PhD interview weekend is structured over 3 or 4 days:
Thursday: Arrive + welcome dinner Friday and Saturday: Interviews, research talks and poster sessions, dinner with faculty one night and dinner with students another night, something fun in the city one day, and a student-hosted party or bar night Sunday: Departure This gives you a lot of time to learn about science, talk to current students and faculty, get a glimpse of what the city is like, and make an impression. The actual events will vary interview to interview, but this is what the majority of major research institutions do.
3. If you talk to a lot of graduate students and faculty and are truly enthusiastic to learn about a program/institution (and science in general), you will come out of a weekend with everything you need to make a good decision. You most likely won't like every interview, but you will start to internally rank them over the course of interview season. Try to go into each interview with an open mind too!
Sorry this is so lengthy - I hope it helps though!
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Some recommendations from a current student interviewer. This is just from my personal experiences interviewing and discussing with admissions committees.
1. Be prepared to answer WHY you want to do a PhD in general. If you are coming straight from undergraduate, be especially prepared to justify why you believe you are ready to enter directly into a PhD program instead of taking a year or two off.
2. Have justifications for why you applied to a specific institution and program. Being able to pinpoint specific faculty, resources, graduate outcomes, etc. all help show you are applying to a program for a particular reason and not just because it is ranked highly.
3. Be able to talk about your research clearly and concisely. If you do not know something, do not be afraid to say you do not know. I would rather have someone answer "I do not know" 10 times than try to make up an answer once. It is also helpful to be able to identify specific things you have taken away from each experience. Also, if you have multiple experiences, it is best to focus on the one you are most comfortable talking about rather than trying to give equal time to all of your research.
Above all, be enthusiastic about your own research, research in general, the program you are applying to, and pursuing a PhD. If you can talk about your research and genuinely seem excited about it, then that will come across to us and we will remember it more than if you can answer every single technical question flawlessly. It is okay if you are nervous and it is okay if you can't answer every question - it is not okay if you are just going through the motions.
4. For faculty interviews, don't worry about knowing their work inside and out. If you want, you can read a couple abstracts from their most recent papers + look at their lab websites, but anything beyond that is not expected.
5. Prepare questions! They can be general questions about graduate school, specific questions about a PIs research, etc., but do not just sit there blankly if you are asked if you have any further questions.
6. If you have a student interview in addition to faculty interviews, be forewarned that at many schools this interview will be weighted alongside your other interviews. This means you need to maintain professionalism and decorum.
7. You ARE being evaluated at all times, but 90% of the evaluation that goes into the final decision is done during the interviews. However, there are really only three things you can do that will get you immediately disqualified (and yes, I have seen each of these happen at least once): (1) Making sexist, racist, or homophobic remarks, (2) falling asleep during an interview, and (3) aggressively hitting on current students or PIs to the point of harassment. Every year, without fail, there are at least three recruits who do one of these things (usually #1 or #3) and are disqualified from consideration.
8. It is okay to drink alcohol if you are someone who likes to drink alcohol. It is okay to abstain from alcohol if you are someone who likes to abstain from alcohol. It is NOT okay to get belligerently drunk and make bigoted remarks or harass current students or other recruits. I would recommend knowing your limits and what type of drinker you are - we want you to have fun but try not to embarrass yourself. Believe it or not, we have accepted people who have gotten black out drunk and thrown up at recruitment parties, but do not put yourself into that situation.
9. Dress to impress for your interview day. A full suit is unnecessary for guys, but some nice slacks, a good button down, and a blazer will suit you well for all interviews. Gals, do not wear heels - you will seriously regret it. For the rest of the weekend, feel free to wear whatever is comfortable.
10. Have fun! All participating faculty and students go into the interview weekends trying to recruit EVERYONE. We want everyone to love our school and our program and want as many people to attend as possible. Talk to as many faculty and students as possible, be engaged, and generally look like you want to be there and you will find the biggest challenge will be deciding where you actually want to go from all of your options. Getting the interview is the hard part - we interview around 8-10% of applicants and accept around 75% of those interviewed. If you have gotten an interview, you have all the qualifications to get accepted - we just need to make sure that you look as good in person as you are on paper.

Thank you for starting this thread. It's nice to have a place to share thoughts with others who can actually understand what we are going through.
This is my first time applying for PhD programs, and I am currently in the waiting period. There are some days where I feel confident in my application and background, but other days where I feel like I have no chance at all. 
I think my greatest worry is that I won't get in anywhere. I applied to ten schools, but wonder if I should have applied to more because most of them are extremely selective. I have a less than stellar undergraduate GPA in my field, which I imagine is a red flag for many schools. I completed a Master's with high marks, worked and conducted research in the field, and am currently a teacher in it, but I don't know if that is enough. If I don't get into any of the schools I honestly don't know what I will do. Getting a PhD has been my dream for over 5 years and I do not have a plan B. I also can't imagine having to tell my letter writers that I did not get in to any of the schools they recommended me for.
My next greatest worry is that I will get in somewhere, but it will not be an ideal location for my boyfriend to find a job. We have been dating for years and currently live together. I don't want to move without him, but also will not turn down the opportunity to get my PhD so I can stay with him. He also wants to stay on the west coast, but I only applied to two west coast schools, both of which are very competitive. We generally just avoid talking about the possibility of me only getting in to east coast or midwest schools, but I feel like it is quite likely. I hate thinking that I will have to choose between my relationship and a PhD.
Overall, the waiting period is extremely nerve-wracking. I try to occupy my time with other things but can't help checking my email multiple times a day. I struggle with maintaining hope but also realism for the outcome. Reading through these posts and simply knowing that others feel the same way helps a lot, so thank you.