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I have built somewhere in the neighborhood of 750 computers, since the days of the Intel 486DX33. I'm currently a computer specialist and network engineer. I will happily pass along my experiences with both Intel and AMD.

Both brands are very high quality CPUs. I have never had a failed CPU from either Intel or AMD. Never.
The compatibility question on AMD is a red herring. There is no compatibility issue, and there hasn't been for many, many years.
Both Intel and AMD have manufactured CPUs with minor design flaws in them over the years.
95% of average home users would never notice any difference at all whether they were using an AMD or Intel machine.
Intel always used to be the leader, with AMD playing "me too". In the past few years, the tables have been turned. Intel was forced by market pressure to make an "AMD-compatible" 64-bit instruction set, and the jump to dual-core architecture was led by AMD as well.
The AMD architecture is more efficient. It can perform more work with each tick of its clock, with less power and less heat than the Intel architecture. Intel largely overcomes this difference with a higher clock speed (GHz), using more electricity and generating more heat.
The performance king of the hill right now is Intel. They have introduced a new architecture (Core/Core2) that is better than AMD's aging K7 architecture. But you pay for it. ($$)
The best value (bang-for-the-buck) is still probably AMD.
AMD systems have been upgradeable through more new processors without the need for a new motherboard.
Multi-core and multi-processor design is nice in certain situations, but the average home user will probably never notice a difference. 64-bit is definitely a non-issue for home use at this time, but they both have it anyway.
Windows 95, 98, Me and XP Home Edition can only use one core, no matter how many you have in the machine. Windows NT Pro, 2000 Pro, XP Media Center Edition and XP Pro can all use one or two cores/CPUs. To use more than two cores in Windows, you must run one of the server versions, which cost hundreds or thousands of dollars.
The amount of system RAM available, speed of hard disk and speed of graphics card all affect the apparent performance of a Windows computer more than minor differences in CPU speed do. In other words, if you save money on the CPU and buy twice as much RAM, a faster graphics card and a bigger/faster hard disk, you'll probably be happier than you would be with the faster CPU.
Bottom line: If you want peak performance and cost isn't a problem, go Intel all the way. If you want the best value for your money, choose AMD.

Not a bad write-up. A bit of quibble with a point or two however:

- The AMD architecture is more efficient. It can perform more work with each tick of its clock, with less power and less heat than the Intel architecture. Intel largely overcomes this difference with a higher clock speed (GHz), using more electricity and generating more heat.

Intel has solved the efficiency problem with the Core 2s, (well, at least the Duos; the first Quadros are still quite power-intensive). They're running as cool or cooler as the Athlon x2s, with less of a power draw.

- AMD systems have been upgradeable through more new processors without the need for a new motherboard.

This had been true for a long time. However, AMD has been changing socket design as often as Intel lately (they're on their third socket for the Athlon 64 family as they finally adopted DDR2), and if I'm reading the presses right, they will have another one when they come out with their Core 2 "killer".

Intel is also closing quite a bit on the price/performance as well. They're not quite there yet though.