Is it possible to run multiple sites under one instance of my application instead of an instance per application?
To clarify I want to run the sites as www.somedomain.com/bar and www.somedomain.com/foo.
There can only be one site per App Domain, which generally means one site per process (which, in turn, means one site per application pool). Consider, if there was more than one site per App Domain, then what would PageReference.StartPage refer to?
You can run them as you mentioned in your subsequent post by creating multiple applications in IIS and assigned them to different application pools. They should run fine like that.