It seems to me the choice would have to be either Mario, Zelda, Grand Theft Auto or Metal Gear. All other series built off of what those four did. Other than the big 4th gen to 5th gen 3D switchover, GTA is the only one that did anything revolutionary with the jump. I mean, as much as I love the Metroid Prime series, they only really added a twist on FPS mechanics, which were of course both revolutionary (and pretty much inaugurated the move to 3D) and primarily developed via new IPs. Though I guess you could say Wolfenstein 3D deserves to be on the above list, if it wasn't for the fact that it doesn't hold up anywhere near the way the above mentioned four do.
For my money it would be Zelda. Ocarina of Time was the first game that felt to me to capture something of a vast open world--a world that felt real, as opposed to the finite boundaries of Mario 64's levels, or the endless unchanging and semi-uninteresting corridors of the first wave of FPS's.
Edit: Duh, none of this counts fighters, I realize. My answer would be the same, but obviously 3D fighters don't owe anything to the other mentioned games. Of course, that change was via an original IP as well.
My consoles and the fates they suffered:
Atari 7800 (Sold), Intellivision (Thrown out), Gameboy (Lost), Super Nintendo (Stolen), Super Nintendo (2nd copy) (Thrown out by mother), Nintendo 64 (Still own), Super Nintendo (3rd copy) (Still own), Wii (Sold)
A more detailed history appears on my profile.
