Best answer I've found to this question is that in some cases you may have a 32-bit and 64-bit version of the same program. For example, Windows 7 x64 includes two versions of IE (I think Vista x64 does as well, but I'm not sure since I've never tried it). The 32-bit version is sort of a "compatiblity mode" for websites that don't work under the 64-bit version. Hence two Program Files folders are needed, to separate the two versions of the same program.
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