A change from a 32-bit to a 64-bit architecture is a fundamental alteration, as most operating systems must be extensively modified to take advantage of the new architecture. Other software must also be ported to use the new capabilities; older software is usually supported through either a hardware compatibility mode (in which the new processors support the older 32-bit version of the instruction set as well as the 64-bit version), through software emulation.
Running 32 bit Windows Applications in a 64bit Windows Enviroment offers minimal performance increases if any, until 64bit application ports arrive its simply not worth it.

I run 64bit Ubuntu Linux with 64bit Applications for this reason on one of my boxes