This is getting interesting! It's fun to see what everyone else uses.
I'm messing around with Scrivener now, too. It seems great, and I think I'll stick with it, but ultimately I'm going to compile things in Word (always have, and as you say, Eigen, everyone else does.)
I've always used EndNote, but a friend of mine mentioned Papers to me, and it looked good. Sadly the functionality isn't nearly as good for Windows yet. (If it does get as good as the Mac version, I'm definitely going to switch to Papers from EndNote.)
For graphing and data analysis I mostly use IgorPro, but in the very near future I'm going to need to start using MATLAB for some things. Even when that happens, I'll probably still do a lot of work in Igor. Thankfully I get both free through my university. I use Adobe Illustrator for line drawings (they come out decent, but take forever). I'm not averse to using MS PowerPoint for quick drawings either... the drawing tools have gotten much better, even if the program isn't exactly what I would hope for in a presentation maker.
Also-- Dropbox and GoogleDocs. Dropbox is how I share papers and data with my advisor and collaborators, GoogleDocs is how I write manuscripts with collaborators.