One thing you need to know is that if a game uses alot of transparencies like Chrono Trigger or Metroid it will run slow. If you turn off transparencies it might not look as nice in some parts but you'll get almost near perfect speed. At some point in a game you can turn transparencies off to get better speed. Also there's quite a few games you don't even need to have transparencies on. My settings are usually:
Transparencies off
333mhz
sound 1.0
Sound 22hz
graphics 1.0
auto framskip off
frameskip 1
Some games i don't even have to use frameskip like Actraiser or Smash TV
Hope this will help you out.