I only had a problem once. The ironic thing is it was the ONE league I WASN'T worried about.
It was a football fantasy league with a live draft at the commish's house. Everyone seemed to know everyone else except for a couple of us.
When it came time to get paid, I didn't hear anything from anyone in the league for a couple of months. Even when I logged in, it showed that the league was basically dead.
After a few months, I finally received a check in the mail.
Like the last poster said, you have to go by what you feel and see. Otherwise, you are stuck playing in some "commercial" league with payouts being at about 70%.... but even with those you have to worry about ringers and the such.
I typically would ask for the physical address and the phone number of the commish. If they hesitate, that's a warning flag.
One other thing, EVERYONE has an email address. I NEVER send money through paypal to a free address such as yahoo, hotmail, and the such.