I guess that would depend on what you were looking to do with your new A1200.
Personally, I'd go for anything with a 68060. I had an A1200 along with a Blizzard 1230 IV (68030@50MHz). Don't get me wrong, it was a great board which added a little speed, and ran games just fine, but it was still too slow for image editing, web surfing, and playing MP3s was definitely out of the question unless you had an additional hardware accelerator for sound. A board with a 68040 will most likely cause overheating issues unless you convert the desktop into a tower case, so that's probably out of the question too. For comparison, I have an A3000/040, and I can at least live with its performance, but would still prefer an 060.
And then there's PPC... :-P
