If you are a "serious" commuter you likely don't let the threat of a little rain keep you from riding. Of course the easiest way to make a waterproof bag liner is to put your stuff in a plastic bag. Then put another plastic bag over that one, with the opening facing the opposite way. Then shove the whole thing into your backpack/pannier/whatever. Works great.
But maybe that's too easy for you. Maybe you've got more time on your hands and you're wondering if perhaps you could achieve a higher level of ghetto style for your bag liner. I feel you. And your solution is at hand.
Over on the Commuting forum at BikeForums.net, member Ya Tu Sabes has detailed his trick for creating lovingly handcrafted waterproof bag liners. You'll need an iron. Maybe two, after you ruin the first one by melting plastic bag all over it.