Currently, on our production IIS web farm, we host about 15 applications in a single App Pool (Default App Pool). There are two websites and about 13 virtual directories.
Besides the configuration time and (maybe) more memory requirements there is no down side to using more than one App Pool.
(Just to be clear... the memory needed will vary depending on many factors -- but there is a way where 15 apps in one pool use more memory than 15 apps in 15 pools. If each app does not need much memory and the apps are used at different times and infrequently.)