The latest version of HeavyMath Cam 3D (3.3) has been released, a $50 program for Windows that enables you to merge the input from two web cams of the same focal length. You have full control over the recording codec, quality, audio sample rate, channel, bits per sample, and bitrate.
The standard version allows you to record to MKA (Matroska Video), OGM (OGG Media), or WMV formats. Additional export choices including Quicktime and MPEG-4 are available by add-on 'booster packs' from creater River Past.
Go here to see the product on the River Past site.
Anyone with experience with this, or other stereo video programs, is invited to weigh in on this. How well do these things work?