Was doing some exploration in terms of the number of application pools for any web server.
Here goes the collection of results.
1) It is good to have one application pool / web application
2) It is also a good practice to run each one of that application pool by a unique identity.
a) In this case we need to ensure that it is tied up to IIS_WPG group.
By doing this we will be benefitted both from security and functionality. It also ensure reliability and availability.Since an issue/error with one application wont cause any side effects to the other application.
I hope this helps!.