history

Qcubed is a fork of the QCodo project which was created by some of the most active members of the Qcodo community a while back.

Since the fork there have been changes on Qcodo and changes to Qcubed which have made them behave differently.

differences in code

Differences are noticable in directory structure.
Where Qcodo has a few directories underneath the webroot by default qcubed has it's supporting directories inside the webroot.

Qcodo has it's own Javascript framework while Qcubed from version 2 up will be using jQuery as much as possible for it's underlying javascript.

differences in style

Both projects have the possibility to generate admin pages, these are both themed to their specific flavours.

differences in project management

Qcodo's source code is currently in github.
Qcubed source code is in SVN

What goes into Qcodo is decided by it's creator: Mike Ho
What goes into Qcubed is decided by a core team of developers.

Qcodo uses a home grown solution for forums / bugs / ...
These homegrown solutions are also available for download as a part of the website.

QCubed uses Drupal for community activities and trac for bugs.

differences in extensions

Qcodo uses Qcodo Package Manager (QPM) for adding additional functionality to the framework.

Qcubed uses plugins for additions to it's core framework.
There seems to be quite some activity and usefull projects in the plugins of Qcubed.  

differences in documentation

While both projects sport a wiki and example pages, Qcubed also features some screencasts which can be good to help people get started, and commenting on API documentation.