While not directly related to emulation, through my experience game programming for Palm OS, I have found that something as 'simple' as accessing an array in a loop can have a HUGE hit on performance. Since your memory emulation is probably an array, try to get the accesses down - try using a pointer, then adding/subracting from that offset wherever you can.

This helped on a Palm, but I guess we're talking different hardware/compilers/etc.