Holy damn.. I think this is the most comprehensively detailed question I've ever seen. You gave us all your specs, you told us what software you had and everything. All my "it must be X" solutions went out immediately, and I'm only down to a few left.

What 3D games? For example, I had this problem with Diablo II but none other. Is it all of them? What bit depth/resolution are you running at? Are the games compatible? Do the games support Win2000? (Likely, but not always..)
EDIT: This really does sound like a DirectX issue. 9.0C? Can you run the DirectDraw/Direct3D tests in Run > dxdiag without a problem?