Absolute best way to clean the iPad screen is dry, with the 3M Scotch Brite High Performance Cleaning Cloth. The cloth costs $3-4, but it is a woven microfiber that pulls fingerprints and dust off like nothing else. I've tried a number of different cloths, including those that came with my HD TV, etc. The 3M flat makes 'em feel like using a paper towel (NOT recommended...). And when it gets dirty? Toss it in the washing machine.
I actually went and bought a couple spares - one for the house, one for my briefcase, and one for the office - just so I'd always have the right cloth handy. The iPad is a great device; I'd prefer it not be a great fingerprint display as well.
I've read to be careful of using microfiber cloths... they pick up lint, dust, debris and if you're not careful you can scratch your screen trying to clean it!
Having said that, we used a micro-fiber cloth to clean the screen before putting on a protector... but we thoroughly washed it out first-- and made sure to use different parts of it while prepping the screen.