The Mocha AE plugin that comes with After Effects CS 6 does a nice job tracking simple planar objects for use in After Effects. By combining this with the Cinema 4D Exchange plugin for After Effects, it is possible to create believable integration of 3D objects in a 2D video.

Links:
C4D After Effects Plugin
Select the plugin under: “Plugins for After Effects CS3 – CS6 <> CINEMA 4D R14 connection”

The video below was created using the following workflow:

1. Import video to after effects and make it a 3D layer.
2. Track object in Mocha AE and export tracking data (copy to clipboard)
3. Create 3D solid in after effects and paste tracking data.
4. Create a camera.
5. Export a Cinema 4D file.
6. Animate in Cinema 4D, aligning work to tracked object.
7. Render 3D objects as png with alpha channel.
8. Import render to After Effects and Finish compositing.

The following tutorials walk you through the process used to create the video above.
The 3rd video below shows tracking for fast moving objects and shows how to adjust the track in Mocha AE.

Tutorial Module 1:

Tutorial Module 2:

Tutorial on Fast Moving Object tracking in Mocha AE

Additional Help

These tutorials show a slightly different method for tracking a square object and I also show how to export the video so it shows up in Cinema4D, which can be a great help for animating the frames that may be impossible to track. This video has a spinning object, and it leaves the frame in a spot, without causing too many problems.

Dealing with untrackable video spots

Previewing the Video in Cinema 4D