Glipper - a great clipboard manager, it's on the repos.
Avant Window Navigator - very slick dock, requires beryl for it to display correctly.
jUploadr - java app to upload pictures to flickr, much better than the official windows one.
Gnome Subtitles - the first subtitle editor in Gnome, to my knowledge, that features video preview. Great little piece of software.
GCStar - want to make a database of all your dvds, books...? This is the right app to do it with.