I have been poking around with Microsoft OneNote recently, and at first glance it appears to be a very powerful note taking app. You can dump stuff in from other Microsoft productivity applications like Word, Excel, and Outlook, and you can even create an Excel spreadsheet directly inside OneNote. It makes taking screen shots easy and has a two dimensional tabbing system that feels just like using a multi subject notebook with the capability of adding as many subjects as you want. I can see this being very useful for students. But with all that power, it feels unfinished to me. You can add notes, draw arrows and circles on top of them for added emphasis, take pictures and highlight the portion of the picture you want to bring attention to, but don't move anything around on the page because all those annotations are just a bunch of independent lines, boxes, and circles. They are not attached to anything, and if you move the big text box, you have to also move all the annotations as well. If you make a correction to your notes in a way that adds space to the text box, you now have to re-annotate the entire page because all your annotations are now in the wrong place. This is a major issue. There is no way to group drawings together (which can be done with the other Microsoft drawing tools), and there is no way to anchor a drawing to a bit of text or a table or an image, or anything else for that matter.
So bottom line is that OneNote is a simple little app that has a lot of potential, and a lot of headache. If you can deal with the pain, it might be able to help you organize your thoughts. I am going to try Evernote.