There are a few things that you may be asking with this question.
Are you asking about the technicial differences between X86 and X64 chip sets?
http://www.amd.com/us-en/Processors/TechnicalResources/0,,30_182_739_7044,00.html
Are you asking about the differences in PE layouts (PE32 - 32bit, PE32+ - 64bit)?
Or are you asing about about X86, X64 and MSIL (agnostic) managed assmeblies?
I will assume that it is the latter. Managed assemblies by default are built agnostic so they will run against the native bitness of the platform. For example, an agnostic assembly running on Vista 64 will run as a 64bit process. You can also target X86 by running on the WOW (Windows on Windows64) subsystem. All x86 applications, including X86 managed applications, can run on Win64.
The decision to use 64bit or 32bit is application specific. Some of the determining factors are: what resources it uses (32bit COM objects, ...), certain performance characteristics, additional address space (64bit), etc.
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