I love so many episodes, my favourite Justice league team up isn't actually in the JL or JLU series its in Batman Beyond. The Call Parts 1 and 2 were so good and I don't think the show ever did a scene as epic as the one where the JLU are saving Metropolis from the planted bombs (also it features one of the only times we actually see Superman using superspeed). The whole two-parter is epic and whilst it has some flaws/continuity issues I can ignore them all. Plus Superman Beyond rocks (we should have seen more of him in JLU).
The two parter episode Twilight is probably the greatest episodes in Justice League seasons 1 and 2 (I'm not counting Starcrossed as I feel thats more of a movie).
In JLU: The Clash has by far the greatest figh I've ever seen animated Superman vs Captain Marvel delivers on every single level and was the best of the entire DCAU. Superman vs Captain Atom and Superman vs Doomsday come very close but not as good.
The massive finale to season two was incredible with the JL taking on Lexiac/BrainThor but the best part for me was the Flash saved the day, as much as I love the big heroes its so good to see someone like the Flash take the spotlight in a major epic story.
There are so many other greats and even the episodes that aren't that great have some great moments still. I miss the DCAU
Yes and as if you can't tell I'm biased towards Superman