What type of software does /sci/ use for research purposes? Things like keeping track of all the papers you've read / are reading, keeping track of citations when writing a paper, etc.
I have in mind more so administrative type stuff, not necessarily things like LaTEX which I already know about. For instance, I'm planning on applying to quite a few PhD positions this fall, and have been reading a lot of papers from various groups and about various topics. I've been just opening them up as new tabs or bookmarking them in my browser, but I think a better approach is out there. If I can't find one my plan is to just have some type of massive spreadsheet document where I can keep track of papers I've read and that can be indexable by date written, date read, author, my own thoughts & comments, or other tags and metrics.
Does anyone have any ideas? What do you use to aid you in your own research?