I once tried to use MAMEWAH against my ROM dump directory (I think it's missing only 1 MAME game) and it works nice and fast.
What CPU are you running? I got a P4 2.53Ghz with 756MB of RAM.
Mind you my arcade machine has only ~125 games broken across a few categories (Classics, arcade, sports, shooters, fighters, racing & daphne).
I can't imagine trying to find my favorite game between 3000 using a joystick!
