Todd Kopriva has collected some resources for stereoscopic 3D in After Effects CS5.5. It’s got all the latest on Stereo 3D for AE including a (text only) document explaining the theory and practice by Amir Stone, the software engineer responsible for steroscopic 3D features in After Effects.
Chris Meyer has the full story on the new stuff in AE, so here’s Karl Soule on how to edit stereoscopic 3D material using Cineform technology in Premiere Pro CS5+. See also the earlier video by Dave Helmley.