The Open Journal
Accepted JOSS papers
The Journal of Open Source Software
A small service that provides the basic Whedon API
Command-line utilities to manage JOSS submissions. May one day be a sentient being.
Papers accepted into The Open Journal of Astrophysics
The Journal of Brief Ideas
Reviews for The Journal of Open Source Software
Package web components in Rails applications using the asset pipeline
Polymer components for writing an interactive online paper (these will probably get broken out in to their own repos at some point but not just now)
MathJax & Node.js. Yes please.
Open Journal for Astrophysics (DEPRECATED). Check out this instead: https://github.com/arfon/theoj