The applications should be sorted in some way. If this is due to my version (from debian testing), just let me know. Got a lot work to do, unable to check that now. Reproduce: Right-click a file, choose "open with"-"other application"
They are sorted: http://git.xfce.org/xfce/thunar/commit/thunar/thunar-chooser-model.c?id=401223479151f999a6913bdaf10ce7bff70dc822