Loved Samurai Jack. In some ways I was happy it ended without resolution, as Jack's slow ongoing struggle against overwhelming tyranny did seem like it could be tied up easily.
Off the top of my head I loved 4 Seasons of Death, the origin of Aku, the robots pumping Aku's evil essence, the Light vs Dark Ninja episode, the one with Jack remembering his past as a little boy, and the ones where he teams up with the Scottish dude.
The Clone Wars shorts Tartakovsky did were also great.