the wikipedia page mentions that cisco pays to MPEG LA royalties on behalf of any software project that uses their precompiled binaries. How do they keep track of who downloaded their binaries and how much money they owe to MPEG LA?
No, it's not only internal use, as long as it's Cisco's binary that's being distributed. That's how for example Firefox ships H.264 decoding support.
The license does not cover any other binaries built from the same Cisco source code, though.
The Wikipedia article is also fairly clear about this and says: "any software projects that use Cisco's source code instead of its binaries would be legally responsible for paying all royalties to MPEG LA themselves, however."