Lester Banks, Motionographer, and Mograph noted some 3D work by Stefan Voigt, who in video and blog posts discusses the basics of how stereoscopic 3D works in Photoshop and After Effects. His tutorials include How to create anaglyph stereo in After Effects and Create optimized anaglyph in After Effects.
Stefan has been using the Optimized Anaglyph Filter, a free Pixel Bender filter for After Effects and Flash from David Shelton. This filter has not been checked here at AEP against the built-in 3D Glasses effect. See Wikipedia for more on anaglyph images, and click the tag Stereoscopic for more resources for After Effects
Here's Stefan Voigt, who also talks about stereo 3D rigs in Cinema 4D and 3DS Max on his blog:
Update: there's another, Anaglyphs With Pixel Bender & Depth Map.