My companies app http://cloudfindhq.com (not open source, so can't see the source code). We have 5 apps, but originally there was only 3 spent some time this week refactoring the code base to make it better structured. Followed the angular generator for yeoman as an example project structure

I think messy code bases can happen quite a lot in angular because it's so flexible, so always need to keep the app structure in mind when programming.

Now our structure is like this

App/ Directives/ Controllers/ Filters/ Tests/ App.js

I think with angular just need to find a structure that works and stick with it, as long as it's consistent it probably doesn't matter.