I have both but my ratio is 20 Intel to 5 AMD, so I guess over the past few decades I have chosen Intel.
AMD's motherboard throughput it excellent, but it still has to shrink its processor dies and increase clock speed to compete with Intel's speed and sheer brute force. I still like that you can build an excellent PC with the lower price AMD processors and Nvidia SLI cabability along with its 64-bit architecture.
AMD have started to concentrate more on the CPU market again as has been shown with their new CPU's running on a 45nm process, higher cache and bigger clock speeds, but it'll take them a while before they're truely able to compete with Intel, they have such a big gap to close. It may be more competetive when the AM3's start to show up when comparing them with the I7's, and AMD always seem to have the price advantage over Intel, but Intel tend to offer more "bang for buck" with what they offer, at least right now.
AMD stuff also works better with ATI GPU's, for obvious reasons, so it's hard to get a board that uses NVIDIA chipsets and allows SLI these days, it's more common on Intel systems. Intel make VERY good chipsets too that allow you to use CrossFire and SLI which goes a nice way to balance things, granted you have to then use an Intel CPU.