Well, it would help in that for the most part, you no longer have to wrap 64-bit data into 32-bit registers, which would save on quite a bit of processing time.
EDIT: BTW though, this doesn't necessarily mean that you can just run an already existing emulator on an athlon 64 and expect it to go faster in that respect. IIRC, most emulators are written in assembly, which means that its already coded to only fill up 32 bits of the registers. An emulator written in assembler would need some significant re-coding just to take advantage of the larger register size, its not like C where you can just tell the compiler to use 64 bits instead of 32.