An ASP.NET web app running on IIS6 periodically shoots the CPU up to 100%. It\'s the W3WP that\'s responsible for nearly all CPU usage during these episodes. The CPU stays pinne
It's not much of an answer, but you might need to go old school and capture an image snapshot of the IIS process and debug it. You might also want to check out Tess Ferrandez's blog - she is a kick a** microsoft escalation engineer and her blog focuses on debugging windows ASP.NET, but the blog is relevant to windows debugging in general. If you select the ASP.NET tag (which is what I've linked to) then you'll see several items that are similar.
If you identify a page that takes time to load, use SharePoint's Developer Dashboard to see which component takes time.
This is a guess at best, but perhaps your development team is building and deploying the application in debug mode, in stead of release mode. This will cause the occurrence of .pdb files. The implication of this is that your application will take up additional resources to collect system state and debugging information during the execution of your system, causing more processor utilization.
So, it would be simple enough to ensure that they are building and deploying in release mode.