Intel and AMD (and VIA, etc.) x86 processors are mostly compatible. There are a few differences, such as in their SIMD and virtualisation support, but that applies to different families from each manufacturer as much as different manufacturers. Software that takes advantage of these features will (should!) work without them too.
From the day AMD brought out their 486, to the day Intel made Core 2, I never bought a PC with an Intel processor - AMD offered better value for money and/or better speed per watt.
I have AMD based computers as well. In the past AMD has *had* to be a better buy or they would not have sold a single CPU. But I think that has changed. With the Core2 Duo I think Intel has taken a commanding lead and literally eclipsed AMD. Of course part of the equation is the price vs. performance, but with the performance advantage of the Core 2 Duo chips, Intel can maintain an advantage without lowering prices.
I recently bought a laptop with an AMD processor, but that was not by choice. The unit ended up on a sizable discount because the model was being replaced with a new one with a larger hard drive. If it had been a model with a Core 2 Duo, I would have bought that. But then it would likely not have been at such a large discount.
To answer the OPs questions, I have seen ***NO*** issues relating to the CPU. I have seen ***MANY MORE*** issues relating to running Vista. In the end I am able to run Vista and get my work done. There are even some advantages to using Vista. I find the networking controls much easier to use than my Win2K machines. But the new security features are so poorly thought out that you need to mostly turn them off.
Jay Leno said the other evening that the cutback notices sent to its employees via the instant messaging system in its OS. Some of the employees will not get the word for many days and some will never get it at all.
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