Separating apps in pools is a good thing to do when there's a reason, and there are a number of good reasons listed above. There are, however, good reasons not to separate apps into different pools, too.
Apps using the same access, .NET version, etc. will run more efficiently in a single pool and be more easily maintained. Most annoyingly, IIS will kill idle app pools, requiring the pool be recreated on each use. If you isolate infrequently used apps you'll impose an unnecessary startup cost on users. Combining these apps into a single pool will make for happier users when they don't pay the startup cost, happier servers when they don't give memory to multiple processes and CPU slices for them, and happier admins when they have to manage fewer app pools.