This article is meant to discuss a few differences between using a single application pool and using multiple application pools in IIS. If you are looking for a more hands on approach for setting up your environment, you might want to take advantage of our paid consulting services http://www.kentico.com/Support/Consulting/Overview, which can tailor a solution for your individual environment.
When using multiple application pools, you can dedicate an application pool to a single site. This will usually keep any problems isolated to one site, instead of spreading the issue across all sites located on the same machine. You can also use different ASP.NET versions on the same machine when using multiple application pools. This is because you can assign a different application pool for each version of ASP.NET. When using multiple application pools, you can use different Windows accounts on each application pool. This can not only enhance security, but it can also help when trying to track down performance issues.
• Your sites will be isolated from each other. So if the application pool locks or has an error, it will only affect the single site.
• You can run different sites under different .NET versions.
• You can have unique settings for individual application pools.
• You can setup unique security features for each application pool.
• Each application pool uses its own memory, which can use up a lot of resources on a single machine.
• It may also be harder to debug the site, since you are running multiple sites in one application pool.
While there are more Pros/Cons for each scenario, this should give you a general overview.