Birth of a Mercenary SE (MotS SP) -
and by extension, ToaM 1 and 2
Not only did it feel like it had succeeded in recreating the Star Wars (ANH/ESB) "feel" (generally and via some nice references), it had plenty of good narrative, good and smooth gameplay and even a handful of nice jokes "How do you turn this bloody thing off!?"
Also, if you ever wonder why a 'FastGamerr' exists, you can
thank this mod for making me end up in TACC and after a few weeks,
register here.
Leeza's Destiny 3 (MotS SP)
These two are the most important JK user-made content for me, and they sort of compliment each other. It also feels very much like "Star Wars" as well, especially in invoking similarities with the Thrawn trilogy and Dark Forces (which in turn I still think is the most Star Wars'y SW game of them all).
If BoaM:SE made me decide to edit JK again and discover TACC (in 2001, even if I had quit playing JK/MotS already in 1999), it was this mod that made me want to make Dark Forces DFM (lol) and thus register here for editing help.
Could go on in detailed fashion for some other entries, but I'll just list the JK/MotS SP levels I really liked during my "second JK era" from 2001-2004:
Liberating Cloud City (MotS SP)
Rebel Agent (MotS SP)
A Pirate's Tale (MotS SP)
Mechanics of the Force (JK SP)
Siege at Vol Kanst (JK SP)
Galaxy of Fear (MotS SP)
Dawn of a Downfall (MotS SP)
Would probably list more, but those were the first ones that popped into my head. Of course, the list could be expanded even further (for instance including all of Goit's projects and Siege on Derra IV) but I only listed the mods I had actually played through before 2005 instead. And even then, the first two are the ones I actually want to be remembered above all.