Is the paper it is printed on clean and bright? Is the letter formatted and addressed properly? Did the candidate hand sign the document?
Paper choice for your cover letter and resume is important. Obvious attempts at attention grabbing are usually viewed as unnecessary. Printing on Yellow, Pink, or Tan paper doesn't make you more qualified for the position. Instead, chose your paper based on its weight - 24lb minimum / 30lb maximum - and brightness - 94 minimum. If thosefigures don't make sense to you, ask the helpful folks at OfficeMax or OfficeDepot and they'll help you out.
I know a question you're dying to ask -- is laserprinting, which usually means a trip to Kinko's, required? Not anymore. These days there are high DPI (600DPI and up) inkjet printers that will do the job just fine. Just watch for smearing.
If you've read Malcom Gladwell's Blink : The Power of Thinking Without Thinking then you know how decisions are made in a split second. Don't give the screener a reason to 'blink' you into the circular file.