I was just wondering what were the best settings for tf2 for the best 3d experiance WITH analygraph glasses.

It depends allot on your tolerance for ghosting.

i use anaglyph on my 32" and i find i get the most stereo, without too much discomfort at about:
-45% seperation
~ -0.03 convergence (fine tune this for preference)
Autofocus ON

TF2 does take quite a hit on FPS tho :S i have a gtx260@700/1560/1150 and it chokes up allot in the start, thought it seems to smooth out after some time