Evernote keeps your notes on a perpetual "tape" in the order that you put them in. You can classify items by "stamping" them with categories, or you can create rules that put items into categories based on key words and such. You can also build task lists and todo's in it and such, and easily search the whole thing. I like and use Evernote, but now that I do GTD I'm starting to see the OneNote (at least the 2007 version with the solid Outlook integration) may be a better tool. OneNote lets you set things up as "notebooks" with sections and pages, which maps very closely to the GTD notion of file folders with sheets of paper in them. One tab for each of your next action contexts, another for your projects, and you're essentially done. If you're tracking tasks in Outlook then you can just mark a OneNote item as an outlook task and it gets copied right over there. If I can see more than one next action available on a project, I'll go ahead and note them in a list, then just mark the very next one to go across to Outlook (provides some of this project/next action linkage some people seem to be looking for). The page tabs along the righthand side become your project list, and the pages themselves the project support material.
I would try them both if I were you. I may continue to run both, using Evernote as my activity log, and OneNote as my GTD/project management tool.