For me, it was perhaps simple-scan, a very simple and efficient GUI to scan documents. I used it with my Brother printer / scanner and it works like a charm. Especially since I do not scan stuff often, so a program with more complex UI would have the effect that I forget how to use it until the next time.
Neverball.
So gaming on Linux is obviously amazing now, but back in 2006 or so when I started using it, it was less than great. I probably tried every single game in the Ubuntu repos and Neverball entertained the hell out of me.
I spent hours rolling this shiny ball around. I loved Marble Madness on NES as a kid, so it was a natural fit.
A close second was Freeciv, as I had also grown up with a copy of Civilization.
Honorable mentions to Nesticle and Snes9x.