The Karazhan Chess encounter is quite unique. While not really a challenge, it wins by being a fun way to unwind in a dungeon.
I really enjoyed the trampoline quest (Jump-a-tron) in Nagrand as a rather unique and entertaining quest. Nothing like a pile of skeletons under a bird's nest and a trampoline on a hill to set you up for an entertaining few minutes...
While not technically an 'encounter' figuring out what triggers Aran's flamewreath has been a source both of huge amusement and frustration for our guild. Among the many triggers include accepting a battleres into a flamewreath (boom), letting divine shield drop while in a flame wreath (boom). And the lowly snaketrap in a flamewreath will forever be a source of amusement for us (in addition to spawning endless SoaP references).
Generally I think Karazhan is a really nicely done dungeon. The boss encounters are all quite different, and there's a fair amount of lore quests for the junkies

. I quite liked the scripted event where Medivh fights the dragon off his balcony. Really my only complaint is I think the trash respawn rate should be toned down a lot. The trash before the Curator should repop every time the raid wipes (it's a gauntlet encounter after all), and the rest should be on a 4hour timer like heroics.
[edit] Oh, I missed one of my favorites: both the Dragon-ride down to CoT dungeons and the Netherdrake flight in Nagrand - big fan of riding a dragon :P