The A4000 is much easier to accellerate, if you want a 'modded' machine take the A4K.
The A3000 is often quoted as the peak of Amiga design, much higher quality case, easy to solder etc, if you want the best 'stock'(ish) machine then the A3K is the one.
I have UAE for 'modded' (since it can go so much quicker than an '060, obscene amounts of memory etc), and an A3000 filled with period extras for the latter :-)