One simple way to make good panniers less attractive is to use them a lot. My Ortleibs, after 10 years of 3-4 commutes/week plus shopping year 'round don't get much attention from anybody. (Of course, you want to start with panniers that will still be usable after that time.)

Edit: my first Ortleibs were 10 years old when this thread started. They have been replaced as primaries but still get used anytime I want front and rear or I need panniers with fewer theft worries. Being Ortleibs, they are as waterproof as they were new and the hardware is easy to get.

Ben