An Application Pool refers to the underlying worker process that is assigned to your web application. The worker processes belonging to a particular application pool will have a set of predefined, common settings depending on the .Net framework version
and the managed pipeline mode. When one sets up SharePoint server, there is a need to create a web application. This web application can be created using an existing Application Pool or a New Application pool can be defined. As mentioned above the worker processes
are defined on basis of framework and managed pipeline. The .Net framework can take values like v2.0 or v4.0 while managed pipeline takes values 'Integrated' and 'Classic'. In simpler terms, to use the capabilities of IIS 7.0 one need to use Integrated whereas
IIS 6.0 or less uses Classic. If you need to understand the exact difference between them then go
here.
Now .Net v2.0 indicates an application pool with .Net framework 2.0 and Integrated managed pipeline, whereas .Netv2.0 Classic has Classic as its managed pipeline.
Now, coming to your question, if no exisitng web application is using the aforementioned application pool then you may go ahead and stop them. The idea of creating application pool is to attach them to a web application so as to define the property of the
underlying worker process. You may open IIS and look at the application pool used by your exisitng sharepoint components (including the central admin) and if they don't use the above mentioned then you may go ahead and close them.
Please refer to the following link to understand setup and deployment of SharePoint :
http://sharepointgeorge.com/2012/create-web-application-site-collection-sharepoint-2013-preview/
and to understand the Application Pool on IIS 7:
http://www.iis.net/configreference/system.applicationhost/applicationpools
Do let me know if this addresses your query.
Thanks,
Vishal