I don't know that I can pick a single favorite, because I see modules as something you "plug in" to an existing game. That means the "best" one is the one that best fits your current game. It kinda depends.
That said, some of my favorites include TSR's B1, B2, B4, the D series, the G series, S4, WG4, WG5, and X1. Also Pod Caverns of the Sinister Shroom and Curse of the Witch Head. I also like the first Rappan Athuk module (the surface and the first three or four levels, IIRC), although I'd convert them (back) to AD&D. The later additions to Rappan Athuk were less impressive, IMO.
As time has gone on I find myself less and less of a module guy, though. These days, even when I use a module I tend to heavily modify it. It's often easier to just "roll my own" in the first place.