Unlimited Adventures
Based on the famed SSI "gold box" D&D games, Unlimited Adventures is a world creation and game design toolkit released in 1993. Despite many limitations, an active community and a number of very enterprising 'hacks' have kept this title active to this day.

War2xEd
Written by Daniel Lemberg, War2xEd improved so much on the basic Warcraft II level editor that Blizzard even began using it internally, and it's considered the inspiration for including a more advanced map editor with StarCraft. First becoming widespread in RTSs, map editors are included with a wide variety of games these days, and are the source of the majority of player content.

Doom WADS
Credited with the first real developer embracement of the modding community, DOOM made quite a splash by incorporating all the media needed for a level into individual files, called WADs. With a central location, community-created tools quickly sprung up to create these files, and id's release of the source code for their editors only fueled the fire. DOOM was also the birthplace of the first "total conversions", starting with Aliens TC.

Neverwinter Nights Modules
Not since the days of Unlimited Adventures had a RPG toolset been released with as much capability as NWN's Aurora engine. Combine the ease of use with the ability to design adventures for single-player, multi-player, and DM-controlled play and you have a recipe for some amazing creations.

Excitebike!
Who says player content has to be on the PC? While a decent "racing" game in its own right, Excitebike really shone because of its track editor. Players couldn't save the tracks, and the design environment was no more complex than combining track pieces in a customized order, but it was one of the first tastes console users would get towards customizing their gameplay experience.

Atari 2600 compiler
A recent development for an archaic system, Fred Quimby's Atari 2600 Basic Compiler is a fantastic example of the lengths that fans will to go to in pursuit of their hobbies. Although the games created using his system can only be played in an emulator, though some fan-made games do still get converted into cartridges, the fact that the community is still active over 20 years after the system release is remarkable enough.

Counter-Strike
The most famous and successful mod ever created, Counter-Strike earned its creators positions at Valve, spawned a retail release - and expansion - of its own, and has earned the distinction of being the only mod that ended up being more popular than the game it was based on. It stands out as the holy grail of mod authors, and as a symbol of independent development.