Don't get me wrong, I love OneNote, especially now that the SP1 build fixes many of the little annoyances from the initial release. As a consultant on the road, lugging stacks of paper around just doesn't work for me and so OneNote has become an essential tool. As well as meeting notes and plans, I write all my blog posts up in OneNote first (I usually have 2 or 3 part-written posts in progress) and then post them up here when I am done.
Despite this, there is one thing that I have come to expect from our desktop apps that OneNote doesn't do. The biggest single annoyance I have is that I can't use the Insert Hyperlink command (or CTRL-K shortcut) to mark-up a word or phrase as a hyperlink. I can do that in just about every other Office app, and what is doubly annoying is that if I use CTRL-K to mark-up a hyperlink in Word, and then paste it into OneNote, it is handled just fine. Go figure that out!