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Yes, they will work fine, 686 is acceptable to install on an AMD system, it won't give you any problems.
If however, you have a 64-bit AMD processor, and you put a 686 architecture on it, it will work just fine, but it won't use the 64 bit addressing the processor is capable of. What that means is you won't get the super high speed out of the 64-bit chip. If it is 64-bit, you'll probably want to get the amd64 installer. Almost all of the major distros have a port to the AMD64 bit architecture.
Actually, you may or may not want to install the 64-bit port. While the 64-bit Debian port is my distro of choice, it requires a lot more tweaking than the 32-bit version. I imagine that within a year or so, the 64-bit OSes will come into their own as far as usability is concerned; but, for the time being, I recommend to my newbie friends that they should buy 64-bit hardware, and install 32-bit OSes.
Since you are somewhat experienced already, partition your disk to allow both versions of your favorite distro, and check it out.
64-bit programs only works best in games, image editing, video editing, sound editing, multimedia playback. Other 64-bit programs provides no performance except what I previously listed. In some cases 64-bit programs perform worst than 32-bit programes. Though an 64-bit OS provides 4 GB or more memory with out any needed workarounds instead 32-bit OS which needs PAE to handle 4 GB or more memory. I suggest waiting until 2010 for 64-bit computing to become a lot better than it is now.