Rod of Seven Parts - I ran this module from '97-'98 with my 2E group. I had to change some things to make it fit into the campaign, but the role-playing element of researching the Rod and its assembly was a lot of fun, especially when a newly-assembled piece gated in a dozen spyder-fiends!

This was a great box, and it's really great that the Rod makes a cameo in the Age of Worms adventure path. I get to dust this stuff off again. I love it.
Return to the Tomb of Horrors - I've had plenty to say about this box here and on Wizards, Candlekeep, and Paizo boards. I started it in '98 with my 2E group, right after we finished Rod. We made it through the original tomb, and our campaign dissolved. I dusted it off RIGHT where I left off in 2005 when I wove it into my githyanki Incursion campaign (Vlaakith searching for Acererak's knowledge of demi-lichdom). An absolutely incredible module. If it were ever redone in 3.5, I'd expect the latter parts to ask for PCs in the epic levels.
Night Below - I ran this with my college group from '98-'00. We made it as far as the Sunless Sea, and they all perished when they decided to go tomb robbing, releasing a drow lich from stasis while plundering a dwarven burial site.
I own both Dragon Mountain and Axe of Dwarvish Lords, but I just couldn't fit them in. I chose to go with the above three modules during my time DMing 2E. Dragon Mountain always intrigued me. So many kobolds, though... Axe didn't interest me much (probably because of the goblins).