Batman: TAS: Almost Got 'Im, His Silicon Soul, Mad Love, Joker's Favor
Justice League: Legends, A Better World, Hereafter, Divided We Stand (they turned Flash from the most annoying character on the show to a badass), The Greatest Story Never Told (Billy West as Skeets? Brilliant!)
The Twilight Zone: It's a Good Life, Nick of Time
Buffy: Lie to Me, The Zeppo, Superstar, The Gift, Once More With Feeling
Angel: Not Fade Away, Smile Time
Firefly: Jaynestown
Life on Mars: Episode one (though I just started watching it for the first time and I'm only on episode 3)
Futurama: Jurrasic Bark, Parasites Lost, Godfellas
The Simpsons: You Only Move Twice, Lemon of Troy
Samurai Champloo: Baseball Blues, War of the Words
Star Trek TNG: The Measure of a Man
Venture Brothers: The Trial of the Monarch (this is when I realized the show wasn't just funny, but that you could care about the characters), Escape to the House of Mummies Part 2, The Invisible Hand of Fate, The Doctor is Sin
Sealab 2021: I, Robot (a lot of those episodes don't hold up... this one does)
Red Dwarf: Backwards, Game Over