Vista x86 has the same issues with 4GB as XP x86, in that some address space will be mapped elsewhere.
The "3.5GB" figure people quote is an average. Depending on the system it can be way more or way less.
Vista x64 will run any software that x86 will run without loss in performance (or at least, without measureable loss, while WOW64 theoretically introduces another abstraction layer it does not need to actually do any work on x64, unlike IA64)
It DOES however require 64 bit drivers. If you are building a new PC this should not be an issue however.
It DOES require ALL drivers to be SIGNED. This means if you want to install any.... umm... illegal device drivers for the purposes of defeating various copy protection systems, x64 is not the way forward atm.
If you buy Vista Retail or Upgrade, then just buy 32bit now and be safe in the knowledge you can switch to the other for just the media shipping costs from MS. If you buy Vista Ultimate Retail or Upgrade, you get both on the DVD.
If you buy Vista OEM, then not only do you need to buy another copy if you ever change your motherboard, but you only get EITHER x86 or x64 and CANNOT switch.