My favorite instance is the Forge of Souls. There isn't anything groundbreaking about it, but the atmosphere is just awesome.
Old Scholo. I miss that place :(
Gonna have to say my favorite instance is Well of Eternity. A decent level of difficulty (for me), and I really liked the various mechanics used, especially for the final boss.
Zul Gurub. I adored the raid, it was nice to have options on bosses, to be able to use mounts, that everything wasn't orange, and for there to be a boss seemingly designed for a bear tank. And mount drops (which later became a challenge to solo for farming). And a fishing summoned boss, and a alchemy summoned boss. Perhaps memories of it as a raid made me like it as a 5-man too. I wish I kept my Nat Pagle's Fish Terminator.
My favorite instance would be Wailing Caverns. Variety of mobs, non-linear route, and gloriously funny chat sessions as those that died could not find their way around to our group (original dungeon back in the day).
Deadmines. Nostalgia trip when the mobs there were Elite, and having problems getting past them just to enter the instance lol.
I would have to say the sun well 5 man just for the lore
Temple of Kotmogu is my favourite instance ;)
My favorite instance is Hour of Twilight. I love killing our leaders.
ulduar and black temple for favorite instance
My favorite instance is Ulduar, by far.
My favorite instance would have to be Black Temple, ive always loved its theme and story, still brings back the good old memories when i run it.
By far my favorite instance is Tempest Keep even though I haven't gotten Al'ar to drop yet... :/
UlduarDefinitely my favorite.
There are so many wonderful ones ... it's hard to choose if limited to 5-mans, but looking at everything, I have to go with Kara. I have so many wonderful memories of learning to raid there with friends and guildies.
Zul'Aman is still one of the most fun dungeons :)
My favorite instance is Ulduar
Maraudon was always my favorite, simply because of all the diverse and beautiful areas it encompasses, as well as the plethora of enemies. And the beauty pageant at the end.
My favorite will always be Karazhan. BC was one of my favorite times and the Chess encounter was brilliant, truly loved that place! Missing it brought me back from a two-year "break" I took just before WoTLK launched.
Icecrown Citadel all the way! I'm a WotLK baby so that was my first raid I was doing semi-hardcore.