I would run sp_who2 to check what processes are using up CPU and if any blocking is happening.  

If you have the money, I would recommend using NetIQ's DiagnosticManager.  It monitors real time stats on your server and it also has a feature callew Worst Performing Queries/Stored Procedures/Batches.  It actually tells you the queries that are performing badly.

BTW, is it happening regularly during the day?

Thanks.