It seems that these days it's pretty much a toss up.
If you want ultimate performance, then yes Intel is going to be better, but you'll pay for it. If you want the best 'bang for the buck' then AMD is probably your best bet.
As for as cores go, unless you use software that is specifically written to utilize more than two cores, or unless you have a LOT of windows open at once at any given time, then you're not likely going to notice any difference between the same speed dual and quad cores. With that being said, Skuzzy has said repeatedly that AH won't take advantage of more than two cores. Basically, it's typically 3D Design software, movie editing, etc. applications this would help with.
The heat difference doesn't seem to be such a big deal anymore. Yeah, typically AMD's ran hotter (except for some of the old P4 chips... ouch), but these days it's all comparable.
So the question really comes down to... what do you plan on using the computer for, and how much do you want to spend? Want to build it yourself, or are you afraid of a screwdriver?