One of my favorites is the episode with King Aquaman wherein all the Justice League members cannot do anything to persuade the would be assassin to confess and then Batman who possesses no super powers somehow gets the perpetrator to spill the beans. I thought that was simply awesome.
My other favorite episode was when the League faced somewhat counterparts from a comic book world. Once again well written and thought provoking. The episode with the android who (no matter what the Justice League did) was no match for them really was great. I commend all the writers of the show for their creative style and talent and I want this show to go on forever.