I agree it's probably best to have each site run under it's own app pool although I know there's a limit to the no. of app pools you can run (I think it's 60) and I believe my servers are capable of running more sites then this limit. The question is whether there are all sorts of implications i.e. security, performance etc of running these 2 frameworks side-by-side as apposed to having them run separately on seperate servers.
These sites are production sites therefore their uptime is extremely important.
ANy suggestions/references would be appreciated.
Onn