Hi blaisedouros!
Thank you very much for this info! As far I know, Sony Vegas can also do motion track, but maybe it isn't as good as Adobe After Effects?
I don't have After Effects myself, but will see what I can do to try out your suggestion!
You are absolutely right about the best way to apply image stabilization is to get it in-camera, but laying free in the water with something like a 100mm macro-lens is VERY difficult to keep steady for half a minute or so.... and unfortuanetly the Fuji W3 doesn't have any inbuild functions to stabilize the image......!
If nothing works, I might try to make a tripod for my camera, but mostly my diving is not predictable enough to know if I will do the recording on a step wall or at the flat ground.... or between rocks, etc....
The very best regards and thank you very much once again from Kim Meineche! :-)
I don't know how smart Vegas is, but I doubt it's smart enough to do 3D stabilization--most standard NLEs aren't. However, there is another amazing program out there called Adobe After Effects which I'll bet you can do it using the following process, or something like it.
Here's what I'd try:
Bring in both video streams to After Effects. Apply a motion tracker to the left video stream, track its motion, and get it dialed in where you want it. Then, apply a duplicate motion tracker to the right stream, but DON'T track its motion. Instead, COPY the keyframes from the left stream to the right stream's motion tracker. Voila! Instant duplication of whatever motion keyframes were applied to the left stream, and it should be synchronized exactly.
Note: This is an ugly workaround, and I have never actually tried it. But, knowing what I know about After Effects, as well as 3D, I believe it should work. The ultimate way to apply image stabilization to 3D is to get it right in-camera, since 3D post is double the work! 
Edited by Kimmeineche, 11 April 2012 - 06:05 AM.