I tend to not run mine completely flat. I noticed that Apple iPods and iPhones which I think have lithium ion batteries usually have a disclaimer about the batteries only being good for something like 1000 complete cycles (which I think counts only if you fully discharge). If you don't fully discharge, it doesn't count.
I've just copied this from Apple's website:
Question: Does the battery ever wear out?
Answer: Rechargeable batteries have a limited number of charge cycles and may eventually need to be replaced. Battery life and number of charge cycles vary by use and settings. As with other rechargeable batteries, you may eventually need to replace your battery.
Question: What is a "charge cycle"?
Answer: Lithium-ion batteries can be charged a finite number of times, as defined by charge cycle. A charge cycle means using all of the battery's power, but that doesn't necessarily mean a single charge. For instance, you could listen to your iPod for a few hours one day, using half its power, and then recharge it fully. If you did the same thing the next day, it would count as one charge cycle, not two, so you may take several days to complete a cycle. Each time you complete a charge cycle, it diminishes battery capacity slightly, but you can put your iPod's battery through many charge cycles before it will only hold 80 percent of its original battery capacity.