Hi
It's a rather old post now.
In version 4.0 you CAN stabilize multiple clips. You just have to select them all from the media list window (using Shift) and take the Stabilize Videos option.
However, even without the option to set up the parameters for Pass1 and Pass 2. of the Deshaker plugin which are available in Virtualdub, the feature as implemented in Videopad works extremely well and for general shakiness the differences between disparate frames is well corrected and no black borders are seen. (Adaptive zoom is possibly set??) Even the virtual dub plugin defaults work well.
If your videoing is so shaky however that frames move about wildly then black borders will be present with the VP settings despite any adaptive zoom present,
If this is the case you can, if you feel it necessary examine each section of such clips after being deshaken and zoom each clip further using the VP effect to remove any black borders that remain. However I would think that if this was necessary then the clips must have been very bady shaken indeed and no amount of "deshaking" would improve matters.
The answer is to use a tripod wherever possible. 
Nat