We plan to add two processors to an existing SQL Server 2000 machine. We don't need the extra processors to handle the SQL Server workload; we're adding the processors so that we can run a small application server on the machine. Do I have to buy SQL Server licenses for the extra processors even if we use the sp_configure affinity mask option to prevent SQL Server from using more than two processors at once?

The short answer is yes. You have to license all four processors even if your SQL Server is using only two of them. This requirement might not seem fair, but it's what the license agreement says.