I have a more traditional Swiss-Guard computer backback. I use a carabiner s-clip to clip the backpack's reinforced handle to one of the seat-rails, ($4, rated for 75 lbs) and then a bungee net ($6) to secure the rest of the backback to the rear rack.

I do a multi-mode commute on a folder, so the pack goes on my back or the train floor for some of the ride, and then on the rack for the long bike ride and the other train. It just takes a minute to do the switch.

-Warr