Okay im gonna recommend you some of my favorites:
Turtle tracks (even tho you might want to wait for deathknight's re-encode because that particular ep was encoded from a bad vhs tape)
Catwoman from channel six
Mutagen man
Hot rodding teenagers from dimension x
Shredder is splintered
Invasion of the punk frogs
Cowabunga shredhead
Usagi yojimbo
Usagi come home
Slash the evil turtle from dimension x
All the euro eps from season 7 (they're excellent imo..except the ones with the aliens...

those are a bit weird, but still good i guess)
I think those are more or less all my favorite eps...maybe i forgot to put some eps, i dunno