realllllJulia

Woo first interview already scheduled! For this program all applicants are interviewed via Skype so I don't feel special, really, but it's nice to get the cycle going. Bring it on! 

Hey all!
My last 4 rec letters came in today so all 7 of my apps are officially submitted. I've gotten the decision from one program already (super early compared to the rest of the programs in my field). I should hear about interviews from two schools in January and have all my decisions by end of February. I'll be over here, freaking out for the next two months.

Just had a phone conversation with my POI at one of my top choices. She said my application was viewed favorably by 3 of the committee members and she is really going to fight for me. I thought it was a great sign but then she ended the convo by saying that those with higher GREs often get accepted first and I might not get a first round acceptance. So I really don't know how to take it. 

Well, till now, I have all of my letters in. Though I still have not got any reply from the departments how late is "too late".
I met my advisor on Wednesday. For some reason, he believed "Generally the deadline for application is 15th", though I sent him the list of programs as well as their deadlines weeks ago. Another fact is the deadline for our department is also Dec 1. I do appreciate that he finally submitted all the letters Thursday late night.
What I learned:
Berkeley (programs using SOPHAS) will allow 7 to 10 days after Dec 1 to complete the application. This 'complete' includes the letters and transcripts. SOPHAS required exactly the same email address: the one you provided and the one the professor registered. Otherwise, professors won't be matched to your request in the system, though they can receive an email. A 10-min talk works way better than 10 emails. Good luck everybody!
 

Some schools also have information on their department websites about this topic. It may be hidden, and not somewhere nice and convenient like the FAQ. I know in one of my fields it is common to allow LOR up to two weeks after the application deadline, but in my other field the deadlines are the same. If you are super stressing, maybe scour their website to see if you can suss anything out. Especially if it's a larger university and has one of those online manuals.
As far as the situation you're in right now. It can be super nerve wracking to be waiting, having done your part, and wanting it all to be set and finalized. It may help to recognize that it makes sense that you're nervous over this, but that once you contact the school(s) you have done everything right. Your professor may know your field better than you do and already understand when their actual deadline is. Even if that's not the case, by emailing the schools you will be taking control of the situation. They will let you know if there is going to be an issue, and from my experience most schools fully understand that professors are incredibly busy this time of the year and tend to drag LOR's out a bit. Most schools seem to plan for that. Even if by some chance your professor has misjudged, it is likely that by contacting the departments they will be willing to work things out with you, and then you can go to your professor with the actual deadlines.
It's hard in times like these to remember that our stresses are valid but also that there's usually no reason to panic. I hope you can get the information you need quickly so you won't have to worry about this.
Good luck!

Too late is when it arrives too late to be considered. So 3 days is probably fine. Many committees will not meet until January so you might have lots of time still.
If a school has a ton of applications, they might do some work in December to collate/sort the files and prepare packages for the committee to review first. If a school doesn't then all materials might go directly to the committee. As long as your materials get to the profs before they start making decisions, it will be fine. 
Some schools may throw out incomplete applications, but I don't think many schools will reject an applicant for an incomplete item out of their control (i.e. if it's missing a SOP then that might be rejected but not if it's missing a LOR). 
That said, what you should do now is to contact the schools waiting for this letter and let them know that your prof has told you he will be a little bit late in submitting the letter. Make sure you contact both the graduate school / university-level people as well as the specific department you are applying to. Don't make excuses for your prof or complain about it or anything. Just state what has happened so that they know to expect the letter a little late.