I don't have any examples, but people keep asking me about this sort of stuff, so I've been working on making some. The idea is that we pick a web site or two, identify a couple of interesting features, and then I clone it. All the while, I take copious notes and snapshot often so everyone can see how it grows from an empty directory into an actual usable site.

This isn't about having yet another Twitter clone (or whatever), but rather having the ability to see one come into being, one step at a time.