for me its currently
uoSNES9X_v0.02y13 for snes and PSP_Genesis_v0.13 for genesis.
I find turning transparancy off has a much greater effect than frameskip for making it more playable, though if the game uses it, then frameskip it is.
for the genesis I find render mode to cell and cpu to 333 helps the slower games out a bit (square button and x button in the menu)