Two great ones are:
DASPRiD - Ben Scholzen released the source-code for his blog as part of a series on modern app architecture. Well worth study as examples of dependency injection, service architecture, models/mappers, even using Phing for build.
Dodo - an open-source todo list by Greg Wessels. A great example of module-based app using layout-switching via plugin and an API module.
Note: Previously Dodo was at http://blog.threadaffinity.com/dodo-downloads/ but now I see no sign of threadaffinity.com at all. If anyone has a new link, I'll update the answer to include it.
