One of the reasons why I had a hard time moving from windows to Ubuntu before is OneNote. I just stumbled upon this Lifehacker article and it reminded me of the application that I always loved.
When I moved to Linux, I wasn't really considering virtualization. I found Basket Note Pads and it served as a OneNote alternative for me. After a while, I stopped using basked and I just settled with Tomboy notes since I am a GNOME user and Tomboy works better for me because it's much lighter and is more integrated with my DE.
When I compare Tomboy with OneNote, I think of the OneNote's many features that Tomboy doesn't. OneNote might not have those wiki-style links but it is much more powerful. You can put multimedia on your notes, the presentation of notes is much better, etc.
Do you think that OneNote is the best note-taking application?