I've written a few scripts that improve the stereoscopic workflow drastically. These are the main features:
* Automatically generate the right view for a scene (using a very flexible camera rig). This relieves you from doing your compositing work twice.
* Create anaglyph, side-by-side or interleaved previews of your 3D scenes, do global mastering like convergence adjustments and color grading and render the final left and right view separately
* Perform elaborate preparation (that is, alignment) and editing of stereo footage
Video Tutorial 1/2: http://vimeo.com/5918877
Video Tutorial 2/2: http://vimeo.com/6094201
If you have done stereo 3D work in AE before, you'll know how annoying it can be and I'm sure you'll find these scripts useful. To get started, please take a look at the info document and my video tutorials. Once you're a little practiced, you can accomplish stereoscopic compositing tasks just as fast as convenient 2D work.
Have fun and let me know what you think about the scripts!