I’m still using both OneNote and Evernote, with OneNote being my reference system of choice, and Evernote being my primary capture tool.
I recently discovered Skitch.
Per Evernote’s website: “Skitch gives you all the tools you need to get your point across faster the first time every time. Use an existing image or capture a new one, then add shapes, write on it, draw on it, annotate it any way you like, and save it to your Evernote account so that it is available everywhere Evernote is.”
I haven’t had the opportunity to use Skitch in any great capacity yet, however the few times I have used it so far, I have really liked it, and think I will be using it a lot more!