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This is the age old debate. But from own experience I can say :
AMD has better floating point calculation. In other words, if you are a heavy plugin/softsynth user, you can generally squeeze more out of an AMD, except when it's specifically written to use SSE2 algo's (and generally it's not the case). Sometimes the difference is flagrant, although since the P4 3.2 the gap has closed considerably.
Don't ask me why, but generally, the whole Intel architecture (so also Mobo and chipset) handle audio better. So if you don't use much plugins, but do a lot of audio recording (multitrack) Intel is still the king.
Most soft manufacturers still test their stuff mainly on Intel based platforms. Sometimes (very rare, but worth mentionning still) something will either work very slow on AMD, or not at all (Steinberg GRM tools only to mention one).
With badly written software (and there are still a lot of them out there), P4 still has the famous denormal problem (in short, for certain calculations, it switches to a high precision mode, which you will usually see as CPU spikes.) CPU spikes in audio, bad news.
Personally, you can't go wrong with either one. Just be sure to check the totality of your setup (so also chipset and memory) as that will be a very important factor in performance and stability.
I'm building a P4 platform myself, because the price difference here is almost nihil, and I'm planning to do a lot of multitrack recording too. That and I still have a solid AMD platform too, so if it screws up I can still jump to the other one 
One mention though. If you're buying now, stay away from the Prescott P4 (those with 1 MB cache). They run hotter than normal 512 kb P4's and at same clock speed they are slower too (like the first P4's were slower than P3's of the same clockspeed).
For Intel based systems, I must admit that pretty much the "standard" right now are the Asus P4P800 Deluxe or the P4C800 Deluxe motherboards. They are very stable, and proven their reliability in studio's. Two major drawbacks though (which is the reason why I don't get it) is they don't run well with the standard PSU from the Antec Sonata case, and have problems with the Matrox P650/750 cards (bios is unreadable, garbled graphics).
For AMD, the "standard" has long been the Asus A7N8X Deluxe. Rock stable and fast with the right memory. Haven't been following the AMD64 stuff so can't comment about that (you won't gain much with that for audio now).
For cooling, the most used right now is the Zalman CNPS7000 ACu or AlCu. Cheap, performant, but most importantly deadly quiet.
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