I was thinking about this very same kind of idea (with OneNotes as the PC-side beast, but any that does good recognition would be fine). Is anyone still actively pursuing/using this approach? If so, how's it progressing/working out?

Xournal's around for OS2008 courtesy of Anidel (new port, much more recent version than the OS2007 version), but the manual on the Xournal web site would have told you about the file format. No SVG.