As a linux user, I've messed around with similar things; there's mind mapping software called
kdissert which I don't actually find useful (my mind is obviously unmappable!) and I think the nearest equivalent to Evernote would be
Basket Note Pads, which I use all the time!
My favourite tool for academic work is the Firefox plugin
Zotero (which works in the Windows version of Firefox too, and has plugins for MS Word & OpenOffice.org Writer). It allows you to snapshot web pages and make notes all over them, highlight bits, keep them in a database for future research, and collect info about the pages that can be plugged straight into your bibliography.