OoT I've never understood its popularity. Metal Gear Solid was the better game in 1998 and should have been GOTY.
OoT was even more revolutionary in terms of gameplay and it used more gameplay mechanics, it's the first console game to feature an open 3D world with a ton of things to explore, the graphics were nothing less than mindblowing at its time, and the game completely blows MGS away in terms of sheer size and content. Really, it's no contest. OoT more than deserved it.
Read the mania: http://www.fanfiction.net/~nonexistinghero In SA2, it's Super Sonic and Hyper Shadow.