I use Tomboy notes and have been synching across computers using Ubuntu One. However, the 11.10 "upgrade" has broken Tomboy Notes and Ubuntu One synchronisation, numerous bugs are reported and it affects a large number of users. Since Tomboy Notes will not be default in future releases I have my doubts this will ever be fixed, since bug fixing has adopted low priority compared to desktop environments. Does anyone know of a good alternative that allows synchronisation in the cloud?
Every software that allows to choose where to save its documents is elegible for synchronization.
An interesting note taking software I would suggest is zim, available in the repos.
You might want to look into "Nevernote" (or "NixNote" as it has apparently been renamed): http://nevernote.sourceforge.net/
It is an opensource clone that is compatible with EverNote: http://www.evernote.com/
There's also an Ubuntu PPA for it: http://www.webupd8.org/2011/03/nevernote-ubuntu-ppa.html
Once you install NeverNote, you can then synchronize it with your Evernote id and access and edit these files on a Windows, Apple iOS, or Android system.