Ganon possessed Ganondorf, and Ganondorf's body was turned into stone. And Ganon had no one to possess so he just stayed in his pig form, which explains why he is in that form in LOZ, AOL, ALTTP, and other Zelda games.
Andross was destroyed in SFAdventures, and he didn't come back in SFAssault. So I would say he is gone. He could come back, but I doubt it.