This all depends on what your going to use the Computer for, some Companies have yet to release drivers for 64bit Windows, but some open source drivers are available, also some games seem to have problems with 64bit, although this is becoming less of a problem.
I personally would stick (at the moment) with 32bit Windows, this will help with Compatibility issues with some hardware,software. Also some people have reported better FPS (frames per second) in games with 32bit than 64bit.
So really in the end it comes down to the usage of the Computer, also as Cohen says 64bit will use all the memory (if you have 4gb+), 32bit Windows Vista(sp1) will see 4gb but only use around 3.2gb.
I have multi-boot Linux/Windows, my Windows is Vista Ultimate 32bit and runs/works well.
Encryptor
Linux rocks the planet...
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