God, I loved the DCAU. So many kickass moments out of those shows.
Some of my favorites:
Batman the Animated Series:
Batman's dream-sequence after being poisoned by Scarecrow:
http://youtu.be/BW1jU_rex8Y
The Joker's eulogy when he thinks Batman's dead:
http://youtu.be/Ld0uIhst3TA
Killer Croc's "Almost Got Him" story:
http://youtu.be/HEdg4glpCkg
The final confrontation with the Joker (okay, this is technically from the Batman Beyond movie, but it uses characters from BTAS):
http://youtu.be/_JEa71aS3oU
Superman The Animated Series:
Clark spills the beans to Lois, kinda sorta:
http://youtu.be/gbQBI1ZMugo
Basically the entire episode of "Brave New Metropolis:"
http://youtu.be/-SMMK8wtwiQ
Superman's final battle with Darkseid:
http://youtu.be/ZVzGyqSbGew
Justice League/Unlimited:
The Question confronts Lex Luthor, only to find out why you never piss off Lex Luthor:
http://youtu.be/9iizKYUNY3I
Shining Knight gets his ass handed to him, keeps fighting anyway:
http://youtu.be/YRiOxDy-HcI
Superman and Captain Marvel slug it out and destroy an entire city:
http://youtu.be/6BJ1-trrgqc