I am often asked the question "What software can I have my students use to make video content in stereo 3D?" There are many options, but here is my short list:
Final Cut Pro
Adobe Premiere Pro and Cineform Neo3D
Houdini offers a free apprentice/educator version of this tool used to make most Hollywood movies! http://www.sidefx.com/index.php?option=com_download&Itemid=208&task=apprentice
Feel free to post a comment highlighting other tools not listed.
On a side topic, if you want to get started now and don’t have 3D projectors and glasses, you can start with what I call a precursor 3D experience in stitched rendered 3D through Microsoft PhotoSynth