Moccalove

1. Yes, that was an inappropriate response
2. Yes, you should discuss the incident with your advisor -- not so much to receive a spanking as to put your mind at ease and figure out any field/subfield-specific steps for going forward (I'm not sure how small your discipline's scholarly circle is, for instance, and different disciplines have different codes of decorum)
3. ...'A weasel and a scoundrel'? Personally, I would print that response, frame it, and possibly consider getting business cards made. 

Unusually way of asking the question (as others have pointed out), but to actually answer what I think you're asking:
I use RefWorks to organize my all academic reading and notes. I have a source for everything I I read (which I usually do by dragging the PDF of the article into it, or I have a "Save to Refworks" link in Chrome), and I take limited notes on the reading within the Notes section of the reference. For things that are really relevant, I'll mark up the PDF with highlighting, notes, etc. and save the annotated version there as well.
Each source is tagged with the subjects (for example, "arabic_syntax", "tunisian_arabic", "negation", etc.), and then I use the folders for projects. So I'll have a folder for the paper I'm working on now, and all the sources will be in that folder. (Sources can be in multiple folders.)
My actually papers and research data is on Google Drive. I write my papers in Google Docs, and I have the Cite with Refworks plugin, so I can just insert the citations and create the bibliographies directly from Refworks.
It's a really great system and I wish I'd come up with it years ago ....

I'm not exactly sure why you're accusing me of either trolling or spewing negativity. I merely said two (edit: three) things:
1) If you haven't heard a yes from Harvard by now, you aren't getting in. This has been told to me by a Harvard professor. They have already made all their calls. That sucks. For you and for me. But I genuinely thought you should all know. 
2) I got my official acceptance from Berkeley. I mistakenly thought that they, like what seems to be the case normally, send out all their official acceptances at the same time. This does not appear to be the case and I apologize if I was misinformed.
That being said, it makes no sense to say this is pure negativity. And with respect to trolling, you'll just have to trust me, but rest assured I have better things to do than to further stoke your fears or induce more stress than you—and I—are already under. I only posted what I thought would be helpful to this board. 

Edit: 
And 3) That Beate Fricke has moved to Bern. She was being mentioned as if she were still at Berkeley, which is reasonable because their website has yet to update. I just found this out yesterday and am upset about it because she looked very cool—even if I'm not a medievalist. Once again, I thought it pertinent to let people—who were discussing her whereabouts—know where exactly she is.