I've used both Evernote and Microsoft OneNote for several years. While there are lots of extensive comparisons of the applications around, I think the difference between them comes down to just a few broad issues.
Evernote has these things going for it:
OneNote's list is shorter:
The folks at Evernote can't quite seem to get their act together. I think the Windows application has been through at least two complete rewrites since I've been using it, each time with the promise that this version will finally be the solid platform on which fantastic new features will be added. But the editing abilities still compare unfavorably to 1990's-era HTML editors.
I can expect, though, that I'll be able to find an Evernote client for pretty much any platform I want, with data synchronized between all of them because of Evernote's cloud focus. Not all of the clients are created equal -- Evernote for the iPad simply refuses to edit notes with "rich" formatting -- but they aren't bad.
OneNote's anchor to Desktop Windows has been its biggest downfall. The cloud-stored notebooks of OneNote 2010 are a great advancement, but Microsoft needs clients for other platforms -- and good clients at that. Even when I had a Windows Mobile phone a few years ago, the OneNote client there was pathetic. I regularly run Evernote clients on Windows, Mac, iOS (iPad) and webOS, and until I can do the same with OneNote, it's hard to imagine it becoming my primary exocortex. That Microsoft has released an iPhone client is promising. Hopefully they'll continue to add other platforms.
Using OneNote on Windows is a delight. Formatting works as expected instead of suddenly flaking out like it does in Evernote. Tables are easy to work with and look good. Images can be resized in-line. Screen clips go into the note I'm editing instead of a separate note, which is the behavior I want 95% of the time.
That Evernote is free is nice, but I've got 80 bucks sitting right here for OneNote if it can make that final jump to universal access.