In another thread (here), I made a comment about Might and Magic 4 and 5 (Clouds of Xeen and Darkside of Xeen). If you installed both of them together, you got a third, new game called World of Xeen that contained the entirety of both games plus extra content that neither game had on its own.
It got me wondering about other game innovations like that. HItman arguably does this with the way it incorporates all three games into the H3 engine. Any others that did this that anyone can think of?