Well, I think I'm over the shock of seeing Rocko's Modern Life in a science fiction poll, so here's my vote.
Tengen Toppa Gurren Lagann. It has universe sized mecha throwing literal galaxies like ninja stars at each other. It also has extremely well developed characters, a unique plot, and completely deconstructs/reconstructs the stale mecha genre but who cares about that. Galaxy Ninja Stars!
Runner ups, in no particular order, are...
Beast Wars
Reboot
Code Geass
Invader Zim