Sorry, I missed the question 1st time around,.... it varies, but for 68k amithlon is probably between 90 and 200% of the speed of winuae on the same hardware depending on what its doing. The heavier the load the faster amithlon is vs winuae. Video is much faster on amithlon, heavier multitasking there's a big difference, lame encoding, video enconding, emulation,etc. all much faster on amithlon.
I also disagree that its possible to build a faster uae box vs. amithlon box. Amithlon can be used on the very latest hardware (Ive used it on both an i5-760 and an i7-2600k as an experiment, although my actual amithlon box is an old 3.86ghz core2duo (which is typically still faster than winuae on my Windows box (the aforementioned i7-2600k) .