Add Everything to my Annotated Bibliography
I think it is somewhat misrepresenting the concept to call it an "annotated bibliography". That term suggests something formal, organized according to a specific, prescribed structure, but really all you're doing is organizing the resources you've encountered along with any thoughts you may have on them. The resulting compilation of information is for your use only, and so you should organize it in whatever way you find most effective. I do suggest using a reference manager, since it takes a lot of the tedious work out of organizing your information, but if you honestly find a Bibtex file or note cards or stacks of paper on your desk to be better for you, by all means, go for it.

Whatever organization you use, it should have a few key features:


Starting from your notes on a paper (or other source), you should be able to easily retrieve the information needed to cite that paper.
And the other way around: starting from a paper's citation, you should be able to easily retrieve any notes you may have for that paper.
Notes should be searchable, meaning that if you remember making a note about some topic or idea, but you don't remember which reference it was attached to, you should be able to find it (the reference) without too much trouble. This probably limits you to some sort of digital database, unless you have a pretty good memory.
You should be able to access the full text of a paper that you've read, given the citation information. If your citation information is complete, this is satisfied by the ability to go on the internet and download the paper.


A bonus feature, not really essential, is the ability to share your notes on a paper with others. Some social reference managers enable doing this over the internet, or try to (assuming your collaborators also use the service), but it's more frequently accomplished by conversations in the hallway.