Ancient orphaned application (almost 10 years old now) which causes problems. It was written back in the day when Java 1.3 was fresh and exciting and Windows XP was still a twinkle in Bill Gate's eye. After installation it wouldn't run due to linkage failure / DLL hell as far as I can tell and even worse wouldn't uninstall itself for the same reason. And this was on Win XP - good luck if you are running Vista or 7.
An open, cross-platform journaling program.
A scientific plotting package.