AfA_OS never had and side effects on both my old Mediator/P96 setup or now BVision/CGX setup. Worked like a charm ever since with no problem at all!
It surely requires an 060 to function as intended and responsive using Anti-aliased fonts and PNG icons across Workbench.
Tools like WarpDT that speed up a lot (systems with PPC) due to fast rendering of Backdrops etc, and HSMathLibs are a perfect example of nice and effective Tweaking of 3.9.