Application pools in IIS isolate applications from each other, so if one application or web site goes does or locks for whatever reason it does not take all other sites with it. Different application pools can also have different .NET, security or other settings specific to that application.
The main disadvantage of Application pools is the extra memory required to run w3wp.exe processes.
An Internet Information Services (IIS) worker process is a windows process (w3wp.exe) which runs Web applications, and is responsible for handling requests sent to a Web Server for a specific application pool – technet.microsoft.com/en-us/library/cc735084(v=ws.10).aspx
Windows 2012 server IIS overview