Here are a few things that should draw up a red flag when you come across an affiliate program:
No Contact Information
If they don't post their contact information on their site then you should not bother with them. To me this tells me they are trying to hide something.
Commission To High
Yes, it is great when we find affiliate programs that pay high commissions. But you also have to be careful that they are not just trying to draw you into their affiliate program by using big numbers. It wouldn't be good to earn alot of money just to get scammed. If it is to good to be true then most likely it is. A merchant will never pay more on a commission then they would get for the sale. It is just not business smart.
Returned Affiliate Payment Checks
If they do send you a check and your bank returns it then this would be another reason to draw up the red flag of being scammed. Of course you should always contact the merchant to try to resolve the issue, it could be an honest mistake. But if it happens in conjuction with no email replies and lousy affiliate support then I wouldn't waste anymore of my time with them.
Read the above lines and keep them in your mind!