Linked Server to SQL Server 2000 server from SQL Server 2012
Be careful when using SQLNCLI10 as described in connect item 

A workaround can be found here

You have to first test the application that is using such SP's from 2012 to 2000. It also depends on where both server's are located and how much data you are pulling out using Linked Servers.

Is there a reason that the other referenced databases cannot be moved to 2012 ?