3D Mark is an excellent bench. If you're using it to compare systems with different videocards you're missing the point, it's worth is using it to compare systems with the same card. Of course a GF3 is going to score extremely high, as it's the only current card that fully supports all tests. That doesn't mean every system with a GF3 is supposed to perform better than another system with a different card in an average game, but it probably will on a game with a feature set similar to 3D Mark.
It's true value is finding large or small performance issues on your system. If you're scoring well below average as compared to a similar system with the same card, then there is a problem somewhere. It may not show up in Quake 3 framerate, or in game x, y, or z...but it will eventually show up somewhere.