Admittedly I haven't played all of the level sets on the list, but I did really like Project H.Y.D.R.O. that one time I played it, mostly for the same reasons Alter-Fox gave. One of its only real drawbacks is it's not co-op compatible, because of how one of the later levels is actually split between a main and a secret level... clever in execution, but it does kind of limit the game modes.
Ironstar and Ironblade are two mission sets I can keep going back to. I don't have as many favorite D1 single-player missions because there just isn't as much you can do with the game as you can with its sequel, so usually it's architecture and execution that I look for in a D1 set and both of those campaigns have some excellently built levels. The "Badlands" level of Ironstar remains one of my all-time favorites.
Konflikt at Karon also stands out for bringing more objective-based gameplay to D2 single-player. Every level feels incredibly distinct and the set has unique design motifs to it, so really my only complaint is the fact that it's only four levels long. But with the atmosphere the set brings, you really get immersed in the world Kruel built for players.
Other than that, I've always been a bit of a DFW fanboy (sheer difficulty of her sets notwithstanding
) and I think it's a great honor that I've got Sirius and DH's help in the level set I'm working on now. The Lost Levels and The Apocalyptic Factor still stand out as some of the most difficult levels I've ever played for D2, but despite the challenge they still do an amazing job of stretching the limits of the game engine and practically reinventing the game itself.