We have a small WSS deployment that we are currently trying to re-organise, we have about 4 or 5 SharePoint application pools for various web applications and the central admin site itself. I decided to look for some best practices for these application pools to try and speed things up, I found this blog post by Joel Oleson – http://blogs.msdn.com/joelo/archive/2007/10/29/sharepoint-app-pool-settings.aspx. All I can say is thank you Joel!
He talks about the correct settings to use for SharePoint app pools – both performance and health. After applying the said settings to ours we have noticed a big speed increase on the server. I recommend you all take a look to make sure your application pools are running effectively.