ATA100 offers higher bandwidth (100Mb/s I believe vs. 66Mb/s) but really doesn't improve the system performance all that much yet because of harddrive limitations (reading the media). In fact, ATA100 is giving me so much problems right now that I just assume going to ATA66...
BTW, ATA100 would probably perform better when large files are being transferred due to higher cache utilization. Or if you purchase a hd with a larger cache, I'm sure ATA100 would begin to show significant performance improvement.