I believe the architecture type (x86 vs x64) is abstracted away for you when making .Net programs, but are there any other considerations that can cause problems?
This article has a lot of good issues to be aware of: http://osnews.com/story/20330/Windows_x64_Watch_List
Personally, my boss has a 64-bit Vista computer, and I program in a 32-bit mode. We've run into the following issues:
Registry for 32 bit apps gets hidden (sort of) into a Wow6432Node folder. Not all apps you are used to finding a path for in the registry will be in that node (SQL Server won't, for instance).
SysWow64 in the C:\Windows folder can cause issues of DLLs not being where they are needed (we had this issue w/ a 3rd party licensing component).
Sometimes the files you need are in "C:\Program Files (x86)", rather than "C:\Program Files". Sucks too.