There are definitely many apps on github to learn from. However a lot of solutions are very unique for particular contexts and everyone is always at some stage in their learning. Even in the best apps you should be able to find plenty to disagree with.
Here's a list of a few notable ones.
This is rubygems.org, strong community effort, has a lot of neat practices: https://github.com/rubygems/gemcutter
This project isn't necessarily best practices, but it's so loud and has so many people involved in working out all kinds of initially-written crap, that it may shape into something interesting: https://github.com/diaspora/diaspora
This is a popular e-commerce rails app for you to build upon. Haven't read the code, but again, it's pretty popular, which means, well supported by community: https://github.com/railsdog/spree
For more check out awesome github's explore page: https://github.com/explore.
P.S. Bucketwise is a Rails2 app created by Jamis Buck (of 37signals and Rails core). It's still worth watching even if you're looking for Rails 3 insights.