If you build this computer for Vista, then you should wait for the release of Vista and then revisit the question.
Make no mistake about that the market will change considerably at the end of July.
Conroe (aka 4MB cache Core2Duo) is initially going to be a highend part. What will happen by August is that the market is going to be dramatically rearranged. 4MB L2 cache versions of Core2Duo will occupy the highend of the performance spectrum. Current models of CPUs will drop sharply in price and fall several pegs down the ladder. AMD, so as not to fall too far behind, is also likely to extend their line upwards with higher clocks. Todays mid-range is going to be lowend, highend will become mid-range and we will have a new highend range.
There is IMO no explicit AMD vs Intel question. Conroe will for a time occupy the king-of-the-hill position for single socket CPUs and dominate the high segment. And at around $500 it seems like the Conroe will be the obvious best choice in August. But depending upon how much money you intend to spend on the CPU you may end up with whatever. I doubt very much Intel will have any general advantage in either running cooler or bang per buck.
The full SIMD hardware width give the Core2 cpus a considerable advantage on benchmarks and SSE heavy applications. So until AMD have addressed this issue, even cheaper, lower performing Core2's should be attractive to people that depend upon such applications. To me, what appears to be really interesting is the day Core2 has migrated downwards, replaced netburst, and you can buy a Core2Duo for ~$150-$200, with performance that isn't crippled by a cut down cache. Core2 is much more attractive than earlier Intel processors because it offers honest allround performance without weaknesses and doesn't run hot or throttles.
Intel was in a position where their CPUs simply didn't sell at all to people that makes an active choice. They could thus afford to reveal the Conroe very early without hurting their sales. AMD is in a completely different position. The only thing AMD must do is to keep their partners adviced about the interfaces of future platforms.
There is today no reason to expect that Intel's longterm future position is going to be all comfortable.
That simply cannot be public knowledge. The very long previewing of Conroe is pretty unique. And the fact that AMD doesn't put on a similar show doesn't mean anything. It's conceivable that Conroe's performance reign will be shorter than the time that excitedable people have been jumping up and down and been waiting on it.
IMO, people who are early adopters of premium parts get poor value for their money. I expect that to be true about the Conroe too. But if you are going to buy a highend part in August anyway, it's probably going to be the best choice. And by a better margin than is usual for this business.