Joking aside, most OS X keyboard shortcuts actually follow a very rational scheme (which is mentioned in the Apple HIG, IIRC). If Cmd+X performs an action X, both Cmd+Shift+X and Cmd+Opt+X will perform similar versions of X, so you don't have trouble remembering "special" shortcuts.
Example: Cmd+Q quits an application, Cmd+Shift+Q logs you out and Cmd+Opt+Shift+Q logs you out without confirmation.
Another example: Cmd+Opt+Esc brings up the Force Quit dialog. Cmd+Shift+Opt+Esc force quits the current application without confirmation.
I don't think this is an OS X specific thing. I suspect Windows, KDE and GNOME all follow a similar HIG.
(No, none of those shortcuts are good for your RSI.)
Perian is hampered in many places by the limitations of QuickTime itself. Apple hasn't yet provided any API for QTX, but they've promised us that it fixes many of our problems. We've communicated with the QuickTime team, and they're aware of our frustrations and seem at least somewhat inclined to work with us once QTX has a reasonable API.