One solution is to get a $20-$40 "screen protector"; you lay one on your keyboard before you close it. They also serve as lint-free screen-cleaners.
After doing some research, I found that the best material for these screen protectors, "Ultrasuede", is readily available and much cheaper when purchased in bulk. So, I purchased a couple yards and used the laser cutter at Instructables HQ to precision cut myself some screen protectors, complete with the embossed image of the Instructables Robot.
Some pics of the finished product are below. Click on the Steps, above, to see how I made it.
Note: You can easily make these laptop protectors with a pair of scissors instead of a laser cutter, as long as you don't mind not having the "embossed" effect on them.
See also Leah's keyboard cover, which uses an old Instructables T-shirt!
Step 1: Get You Some Ultrasuede
I even found some that's not too far off from the Instructables orange. Bonus!
Note: User Sinner3k suggested that eBay might be a good source for ultrasuede. I looked around and found that he was right. Ultrasuede remnants (perfect sizes for this project) can be had for a third the cost of what I bought it for!
Step 2: Figure Out Laser Cutter Settings
For the raster cuts, I wanted to know how much contrast (burn) I could get without creating a rough surface on the Ultrasuede.
For the vector cuts, I wanted to know how much power would cut the Ultrasuede, and how much would simply score it.
Step 3: Set Up Your Design
Step 4: Cut Out Blanks
Note: The notches at the lower left and right hand side of the screen protector are to make room for the rubber pads on the top half of the laptop. They also happen to look cool :)
Step 5: Burn in the Image
They came out really well! No more scratches on my screen...