Sql server 2000 32-bit would run fine in a Windows on Windows (WOW) environment on the 64-Bit machine,
however There is an known issue on creating a linked server back to SQL2000 (32-bit) , one of the system stored procedures needed to update before getting the distributed query. Here is the link of the MS KB
http://support.microsoft.com/kb/90695[
^]
My advice If you are running a 64-bit version of a Microsoft Windows Server operating system, you need to use SQL Server 2000 Enterprise Edition (64-bit)