You have to keep Dungeon out of this! There are just too many cool adventures in that mag! Its why I subscribe to it 3 years at a time.
OK, I own the vast majority of modules out there. I own everything everyone has done except for Goodman games and I only have 8 more to get there. Easy for me to do since they are either all still easily available or will be soon reprinted by Goodman (I'm not a collector in terms of "Mint original issue" collecting, I am a "completist" collector)
There are a lot of good modules available. NeMorans Vault is a very cool adventure, so is Giants Skull. I really wish FD would get back into module writing. I also like several MonkeyGod modules, in particular Black Ice Well (it has Slaad in it!), I like Kenzers Coin Trilogy a lot, 3 Days to Kill by Penumbra (several others of theirs are very good as well), several of the 3E modules by TLG, Winter Rune has become my favorite. Freeport, especially when everything is taken together (even the DCC), is very good.
Then of course, there is Necromancer Games. I have a long list for them, because I at least "like" every module they have put out, even the ones put out through Kenzer. The ones that stand out to me are: Lost City of Barakus, Grey Citadel, Hall of the Rainbow Mage, Rappan Athuk, Tomb of Abysthor, Crucible of Freya, Doom of Listonshire, Morrick Mansion, The BoneGarden, Lost Caverns of Thracia (Judges Guild redo) AND (despite trancerjeremy's opinion) Trouble at Durbenford. There are even more exceptional ones in Vampires and Liches, Dead Man's Chest, etc...
So there are plenty of exceptional modules, and many more of simply "good".
I probably should also mention the "Witchfire Trilogy" from the Iron kingdoms people. I never ran it, but I sure did enjoy reading it.
I can't pick a "best one", they are all very good for different reasons. If your looking for the one that has become a "campaign fixture" for me then that would be Crucible of Freya's Fairhill, Lost City of Barakus' Endhome, and the Grey Citadel (Don Eamon). With Tomb of Abysthor and Rappan Athuk being dungeons in any campaign world I use.
Plus I have gotten to read the "rough" of the sequel to Grey Citadel, the "Eamonvale Incursion" and I am going to love Don Eamon even more after this module comes out, whenever that will be. At least 6 more months I would guess.
Now there is a company who did a bunch of modules that were "OK", none of them I fell in love with, but I am totally blanking on who they are. I'll have to go out to my garage and look at them.