QuakeWorld Improvements, Netmech+, Angband, and thats just from the 90s. Its fairly common, and has mixed appeal.
QWI (who also made QuARK, that was incorporated by iD as well) was very upset about it.
The Netmech/Mechwarrior community on the other hand was very grateful to Activision for adopting its improvements and allowing its models into the base game.
A number of "improvement packs" have basically turned into "remasters" as well, though thats a little different. Like Ultima, Baldurs Gate, Planescape, etc.