If you are running entirely at stock settings, and you have already allowed for the MHz difference, then Xilikon is correct, the only real difference is the FSB, which does have a small impact on performance in some apps.
If you are planning/willing to overclock, then the most relevant difference becomes the CPU clock multipliers...
E4400 = 10x
E4300 = 9x
E6400 = 8x
E6300 = 7x
So the E4400 is actually the easiest to overclock while the E6300 is the hardest by far.