Yes, but the problem with this is that you can't just enter a stream of text. If I'm in a math class, attempting to take notes, I have to point and click on those apps.
With apps that support LaTeX, I can just type $, start typing math, and type another $ to go back to regular text. Sure, I'll have to type things like \int, but that's still faster than trying to find the integral button in OneNote.
I recently moved away from Evernote for this reason and the slow client. The one thing Evernote has is the websync and webclient but between Dropbox (latex in text files), Gmail and Google Docs I get pretty much the same functionality.
It makes me sad, because I live on linux and notetaking apps there are mediocre. The best I could find is keepnote.
Onenote is years ahead of everything else, but I don't want the vendor lock-in and the binary files that it produces.
Evernote moved to .NET 3.5 so no wine support. Bah!