Honestly, here is where I would break it down...

A5000: Wins hands down in effects, very easy to use, not many options to add, memory is cheaper using more readily available 32Mb 72 pin SIMMS...126 note polyphany, 32Midi Channels, Fairly good filter sets, great overall quality....

E6400: Incredible Filters, very impressive architecture, more flexible preset structure, beat munging, more control in sample editing, ability to use large cheap internal hard drives (I have a 13.6 Gb in mine), to get effects as good (they say better) than the Yamaha will cost you $500-$700, wont be available for a few (should be soon... To get 128 Polyphany costs around $500, and to get Digital I/O, extra 16 midi channels, and an ASCII keyboard interface for remote control costs $300 (all one upgrade)

All things considered, you get more bang for the buck with the A5000, but if you shell out the money, you would eventualy have a better sampler with the E-mu IMHO Both are very good pieces of equipment