One could possibly count the sprawling mods that came out of Witch Trainer and Rogue Like? Witch Trainer: Silver and Rogue Like: Evolution are practically separate games-- especially WT:S, which more than just adding assets like the other I mentioned, adds actual mechanics on top of Akabur's original game. And Rogue Like also gave rise to the modernized, and frankly much better (so far), Null Hypothesis.