I've heard of two different products used (one of the arcade guys I talked to in the Build Your Own Arcade Controls forums was an arcade employee)... he said for a quick and dirty setup where they didn't care about future quality, they used all-purpose drywall joint compound. For a stronger, more permanent and better joint, they used subfloor patch like this. My brief stint with a flooring contractor we used a product called Plan-It Patch and I can see the benefit of it.

Bren R.