It's not the software it's the owners of the company and the people who speak for them. I run a search here (unless I already know) and read some of the posts from the owners and their reps (Attitudes often trickle down) to see how they view affiliates and the industry as well as their general character. I often find myself going with my gut about a company. I've been in the industry since before 2000 and even now I've only ever been stiffed on a payment one time and that was when I first started. So I must be doing something right.
Overall I like a 100% ccbill program best because there are less things to worry about not to mention the minimum payment and payment delay issues being eliminated. But I know for a fact even ccbill sponsors can and do cheat affiliates. Based on stats alone I like nats 4.1+. It's miles ahead of anything else I've seen and there have been some major improvements in recent versions.