As far as I know, it's just bubbles of Nitrogen gas. When you crack your knuckles, the bubble bursts into tiny bubbles, making a cracking noise. The gas is still there in the joints, but because it's in the form of many tiny bubbles, your knuckles don't crack. If you sit around for a while, those many bubbles reform back into a big bubble and you can crack your knuckles again.

Don't take my word for it though - I'm not an expert. I have read about it and this is what I remember off the top of my head.