Dedicated app pools typically will keep problems occurring in one site from effecting the others. If you share app pools across sites, you could bring down all sites on the box when an error condition exists for only a specific site (or app pool).
Also, if you are mixing versions of ASP.Net on the same web server, you will need different app pools per ASP.Net version at a minimum, or do it per website.
I can't think of a good reason not to separate app pools, it is so easy to do.
The primary reason for combining sites in app pools is to conserve memory. There's a large memory overhead in running several w3wp.exe processes. If you have no specific reason for splitting them up, it's better to keep them together.
Also, you can designate different users (such as a Windows account) for different app pools. That enables setting up those users with different permissions in the database. That helps enhance security, and enables tracking which website/user is hitting the database, useful when tracing database performance issues.