Technically 2000, but Sacrifice. It's still one of the most unique games I've ever played, and is my top wish for a remake/remaster.
It's a hybrid action RPG and RTS, which isn't completely unheard of, but even in its niche genre it's unlike anything else. You play a wizard with a range of both spells and summonable units, which can be ordered around to a limited degree, or more commonly used as a personal escort. Both the units and your own spells are very creative, and the higher level ones can be ridiculously powerful. In a glorious early celebration of terrain deformation, many of the high level spells will create volcanoes, mountains, craters, or even gaping voids in the already surreal landscapes. The story mode is also very weird and funny, with some top level voice actors.
Legend of Zelda Ocarina of Time. Super Mario 64 was my first "3D" so to speak, but OoT took that to the next level. The feeling of wonder when I first left the Lost Woods and came out into the field will never be topped.