I've tried just about every setup-- panniers, trunks, backpacks, messager bags--- currently I have Performance trunk I got for my B-day. It works OK for my needs, but I don't lug around computers and ride in street clothes.

My favorite is a Wald wire basket on top of a rear rack. It's cheap and not likely to get ripped off. You can really carry a lot in then-- I like them for shopping, taking a empty day pack and filling both the pack and the basket with food for a short ride home.

For commuting I like to toss a daypack into the basket and tie it down with an old tube. If you have to lock for bike up outside or in basement, you can just take the backpack with you. Easier, quicker and cheaper than messing around with panniers.