Q: What is an acceptable number of virtual machines (VMs) that can be managed through System Center 2012 App Controller?

A: There's no hard limit to the number of VMs that can be managed through App Controller, although typically when reaching over 2,000 VMs I have found the interface starts to slow down. I have also seen environments with 20,000 VMs; however, they tend to have some serious performance issues.

The specific App Controller limits are detailed at the Microsoft website.  However, these relate to numbers of management servers, concurrent uses and more,  and not an actual number of VMs.