I just had a look at the site of of the player used

http://developer.longtailvideo.com/trac/wiki/Player5PluginsBuilding

As far as I understand one can script the player with Actionscript and interact with JS.

That means a simple webpage with two "raw" videos side by side, which are simultanously started and controlled with JS-Buttons should be possible.

AFAIK VLC is already a sufficient and cross plattform solution to record a screencast from a laptop.

Like this it's only a question of synchronizing the videos by the audio track when uploading.

Having external JS-Controls to interact could even help the audiance to further tune the synchronization.

I think that could be a good KISS solution for the start... :)

UPDATE: As a bonus it should even be possible to synchronize a PDF or S5 presentation as long as the timecodes of slide changes are logged while presenting.