Mine without a doubt is Thief 1&2 fan missions, I have been playing them since 1999 and the community is still very active and new fan missions are being pumped out, all while Thief visuals have significantly improved since 1998 thanks to new versions of NewDark. There's hundreds and hundreds of fan missions and from my experience at least 5% of them ary very good.

In second place I am putting Heroes of Might & Magic II&III fan-made maps.

My third place goes to Fallout 3 and New Vegas, some of the user mods make them so much better, like play after main story and unlimited companions.

Total War mods are the most impressive pieces of fan-made content i've ever played. Especially for Medieval 2.

My favorite fan-made content is the following: Brutal Mario ( SMW romhack, not complete), AM2R, Left 4 Dead 2 mods, Sonic The Hedgehog: After the Sequel, Mega Man Unlimited and a few others.

Zak McKracken: Between Time and Space

Right now Another Metroid 2 remake, I'm still amazed at how good this game is for a free fan-made project.

Duuude, I couldnt get it on time be4 it went offline because of Ninty... Is there a way to still get it?

BTW, my fave Fan content has to be Dota, the original, as it was a mod for Warcraft 3.

Of course, I'm uploading mine and I'll send you the link in a private message.