What protocols are built on top of Bitcoin?
New information: 

See David Schwartz's response at examples-of-asset-backed-virtual-currencies for a short description of Ripple.

Older information:

The List of all Cryptocoins  mentions both Mastercoin (MSC) and Ripple (XRP).  This URL is dated, and Ripple is now open sourced. The ripple video is informative.  According to Wikipedia, Ripple is currency agnostic. Ripple has network consensus times of 2 to 5 seconds (which is much less than 2.5 or 10 minutes) and already has 100 billion units of XRP which probably explains why it is not visible at Mining Revenues. I've yet to dig into the Bitcoin Ripple Open Forum.

The Central Banks are scared that an open source architecture is emerging that will be redefining the FIRE Sector, and thus threatening their monopolies.  The FIRE Sector is starting to go through a very disruptive innovation revolution with the genius of Open Source Technologies. If these distributed technologies are implemented properly, we could be on the verge of another 1776. I would love to see the diagram below updated and refined by the Open Source Community so we all have a bigger picture road map to focus our efforts.