I've read mention that there's some software that may not run well on an 040 or 060 system. Is this a concern? How big a concern is this, and how well can it be worked around ?
I've been using an 060 for a number of years now, and their is very few progs that don't run correctly with the 060.
The odd one or two that didn't were easily sorted with the c: drawer command CPU060 available from Aminet, for switching on and off 060 caches...

(the only thing I haven't been able to get working is Pinball Fantasies AGA, even with WHDLoad..)