Stereo3D Toolbox from Tim Dashwood is a new FxPlug filter designed to work with After Effects, Final Cut Pro, Motion, and Final Cut Express. It requires Mac OS X 10.5 (Leopard) and a supported graphics card.
Built upon technology from FxFactory, Stereo3D Toolbox lets you output "media to a wide range of Stereoscopic 3D formats (side by side, over/under, checkerboard, interlace, anaglyph) as well as manage the demuxing of side by side, interlace and over/under formatting. Comprehensive compositing features and capabilities include keyframeable x, y, z axis convergence, individual left/right eye scale, color correction, selective flip/flop, reframing and 'auto scale' compensation."
They have several tutorials up already; this one that demonstrates how Cineform Neo3D works and how to add Stereo3D Toolbox to Neo3D muxed clips:
Update: Fxguide.TV (#64) talks with Enrique Criado on the different aspects, both technical and narrative, of stereoscopic production.