This is difficult. As with some of you, I've been playing since vanilla, but my recollection of the instances isn't too shabby. I can't really say that one instance in particular stands out for me, but I'll do my best.
Vanilla: Maraudon, Scholo, Strat Live and Upper Blackrock Spire.
- Maraudon was really diverse and is split into three parts: orange, purple and the waterfall area. Unlike a lot of people who had trouble finding their way around, I did it enough to familiarise myself with all of the areas, and enjoyed almost every part of it.
- Scholomance was very cool and actually somewhat challenging in low level gear. I especially liked the four bosses down the bottom that you had to kill to bring out the schoolmaster. And who can forget trying to pull Rattlegore without adds.
- I preferred Strat Live over the dead side. Firing the cannon was cool and I prefer fighting humanoids over undead. Can't forget about Timmy the Cruel, either.
- Lastly, UBRS has to be in my list. Sneaking past the eggs, killing Rend, the Beast, kiting Drak - it's an epic instance.
The Burning Crusade: Mana-Tombs, Shadow Labyrinth, The Mechanar, and Magister's Terrace. Outland had some truly challenging dungeons, especially on heroic. They were also very fun with great boss mechanics in most. Shattered Halls comes in second place because I enjoyed the gauntlet, and the other two Tempest Keep ones also come in second place because they were fun.
- Mana-Tombs was challenging. Like a lot of TBC instances, CC was quite important. I liked the bosses, especially how difficult Nexus-Prince Shaffar was, and the escort quest made you clear the whole instance before attempting.
- Shadow Lab - Fun with party-wide mind control (Blackheart), kiting Vorpil away from the shades, and then there was Murmur's room. What a challenge to clear! I liked doing Murmur on heroic. It showed how quick people's reactions were.
- The Mechanar - no one liked the Sepethrea fight. Those elementals did some serious damage! Pathaleon was a real challenge too. The whole theme of Tempest Keep with its glowing lights, Draenei architecture and abundant magic was a great experience.
- Magister's Terrace was obviously added in the Sunwell patch, near the end of this expansion. It was definitely challenging. The randomness of Priestess Delrissa's companions and the anti-gravity phase / burning down the phoenix of the Kael'thas fight made for real challenges.
Northrend: The ICC dungeons. Sure, other dungeons have their appealing fights, such as transforming during the Tharon'ja battle, or -all- of the fights in the Nexus - which makes me consider that the Nexus is probably my second favourite instance area; including the Malygos fight. But the ICC dungeons are polished and the theme of them circulates around the core of the expansion: the Lich King's presence is palatable. They are about as challenging as Northrend dungeon content gets (which isn't saying much, really), and the boss fights have some fun mechanics. The Halls of Reflection gauntlet is much improved over the Shattered Halls one from the previous expansion.