I have the same problem at work, in that we occasionally have high server loads but I have no idea how to establish what scripts (and what aspects of those scripts) are causing the problems.

One problem with benchmarking the scripts is that this may not tell you the whole story - if they connect to a database, for example, the efficiency of their database requests will primarily affect the processor use of the server process rather than the script process.

In my case, I suspected database load was the main problem, so I hacked the database abstraction used by the perl code to log the SQL of every request, and started going through looking for requests that needed indexes, and duplicate requests that could be cached. I found a surprisingly large number of opportunities for improvement, and the system administrator hasn't complained of server load since, so I'm hoping that means I've improved things. :)