2 different methods here:
One is just a pillow touching both heads. I REALLY HATE the wierd resonances/sustained notes you get with kicks that are dead, so this is preferable for me. If I need a long kick sound I'd rather add a static sample.
If I'm doing something more on the indie rock side though, I get a basic beach/bath towel. I fold it in half lengthwise, and then widthwise. Lay it in the bottom, generally speaking there should now be 3-4 inches on each side of extra towel. I then fold that over and push it against each head. Seems to control it a little without losing much.
a third thing which I've seen done, but don't do myself is some guys I know just lay a pillow against the outside head. When you hit the kick drum the pillow jumps off the head barely and then settles again.