I love instances. They're far and above my favorite part of the game -- I'm definitely a co-op PvE kind of player, and PvE instances are, to me, what's really great about MMOs: a group of players can sit down, and in an hour or a few hours, take down dragons, kill some monsters, and nab some epic loot.
And of course I've had lots of bad instance runs. But today we're not talking about good or bad -- we're talking about the best. What's the best instance run you've ever done? If "best" can be described by how much loot you get, then a recent Naxx run probably meets the criteria for me, as by the time we'd toppled Kel'thuzad as a raid, my Hunter had picked up at least four epic upgrades (and gained probably a good thousand DPS along with those). If "best" means most fun, I can think of some old UBRS runs back in the day in which every single one of us knew the instance and each other so well that we weren't so much fighting bad guys as just hanging out and telling jokes while picking up loot.
If "best" means most exciting, then I have to think back to BlizzCon a few years ago, where we got our first hands-on of Wrath of the Lich King. I went into Utgarde Keep for the first time ever with a few guys from the press room, and though we only made it to the first boss (and I don't think we even beat him), I was just so fascinated by all of the new stuff we were seeing, my first look at the Vykrul and the huge Forge in the entryway there. So "best" can mean anything -- what's your best instance run?