Many of the Epiphany integration ideas above were first discovered (or in some cases, the integration functionality was coded into Epiphany itself) by the author while creating the Popup Blocker extension.
While writing an extension, you will almost certainly need to keep looking around epiphany/src/ephy-window.c, epiphany/src/ephy-tab.c, epiphany/embed/ephy-embed.h, and others. The code is very clean; if you still have questions, IRC is a great place to ask (see Getting Help).
You may come up with great ideas when writing your own extension. Feel free to email the author some sample code; a new section could be added to this document to help other extension writers.