32 bit apps will run on R2 servers. Windows does this with WoW64 (windows on windows). You don’t need to do anything special to enable this (not cure on core). There is also a separate space in the registry that holds 32 bit app registry settings.
32-bit applications can be run on the core installation if you enable WOW64. If WOW64 is not enabled, you will simply get an error message that the system cannot run 32-bit applications.
The only exception to this is if you are using IA64 processors as IA64 doesn’t support WoW. However if you use x64 processors (which 99% of people do) then you are fine.