I have an application which is developed in Symfony2. Now the structure for it is as follows:
There are no hard and fast rules on how to structure your app using bundles, but here's what I came to after developing on Symfony2 for close to a year.
Use one app specific bundle. At first, I started with multiple bundles like CommonBundle, UserBundle, MainBundle, BlogBundle, ContactBundle, etc. That proved to be not so convenient in the end, so I switched to just one app specific bundle — AppBundle.
You can organize your code neatly using subnamespaces. For example, the backend controllers would go to the AppBundle\Controller\Backend subnamespace.
Note that I'm talking about one app specific bundle — that stuff that's unique to the concrete app and won't make sense to reuse elsewhere. You can still develop separate bundles for reusable stuff and put them into the vendors infrastructure.
Keep non Symfony specific stuff out of bundles. There is no need to have a bundle for the model and the Service Layer classes in a bundle if they are not Symfony2 specific. See this question and my answer for further details.