Here's a couple of projects that I've been personally impressed with. I hope you don't mind a non-Github repo in there..

C

  - REDIS @ https://github.com/antirez/redis
  - Postgresql @ http://git.postgresql.org/gitweb/?p=postgresql.git;a=tree;f=src;hb=HEAD

Java

  - Spring Framework @ https://github.com/spring-projects/spring-framework
  - Guava @ https://github.com/google/guava

Javascript

  - ui-grid @ https://github.com/angular-ui/ui-grid

Can't say I agree personally on UI Grid - it's a bit of a mess in some ways, especially in its distribution. It is also a bit of a configuration nightmare.

For high quality JS, I would look to some of the major frameworks out there:

https://github.com/facebook/react

https://github.com/angular/angular.js

https://github.com/angular/angular

There is a lot one can learn about software design by reading the source code of major libraries, and is far more reliable than any third party library in the ecosystem.