Binary package hint: notify-osd
With some of the fonts set as an "application font" via System -> Preferences -> Appearance notification pop-ups are displayed with Deja Vu Sans Book (i.e. the default system font).
Though they are meant to be displayed with the "application font".
I've attached two screenshots of a correct behaviour (with Droid Serif) and an incorrect one (with URW Bookman L).
(Not that I would use serif fonts for UI — it's just to make the difference more noticeable.)
I've chosen two fonts available in the repository to insure that this behaviour is not a result of an incorrect manual font installation. But it is reproducible with fonts just dropped in /usr/share/fonts/truetype folder: for instance, Segoe UI or Lucida Sans Unicode work OK, while Lucida Grande or Nokia Sans Wide are replaced with "Sans".
The only pattern I notice here is that fonts with spaces in their file names do not work (not sure about URW Bookman or URW Gothic — I don't know their filenames).
DistroRelease: Ubuntu 9.04
Package: notify-osd 0.9.11-0ubuntu3
Uname: Linux 2.6.28-11-generic x86_64