I use a
leather case from Monoprice. It's not bad for $10. The only faults are that the stand portion of it doesn't really work as well as Apple's smart cover and the magnet in the flap seems to be too small/weak as any fidgeting of the cover causes the device to wake up and go back to sleep. You'll hear it click a lot (the lock sound) if your hand constantly brushes up against the flap.
As for cleaning it, I just use whatever soft piece of cloth is near me... including clothes that I'm wearing. I do the same thing to my phone, and it works just fine... no weird micro-scratches or anything like that.