Firstly, you will want to check out the reputation of the company with which you are getting involved. One simple way to do this is to check out the online discussion forums. Is there a real person behind the affiliate program? If there is a big name behind this product, then simply Google their name to see what you come up with. They may have previous products or services. What are users experiences of this particular marketers past products?
I personally know of a handful of internet marketers whose products I will buy time and time again, simply because of the superior quality of their products and their tendency to over-deliver. So, from an affiliate marketers point of view, it makes perfect sense to sell the products of someone who has built a reputation online. Why? Simply because their offerings will be much easier to sell.
Another thing to check out for is the amount of commissions that is being offered by this particular merchant. For digital products it is not unusual to get between 50 and 75% of the sale. Digital products have very little overheads - so the merchant can afford to offer really high commissions. Any less than 30-40%, I wouldn't even bother promoting, unless it was a high priced item with a high conversion rate.
Many product owners will provide you with the clickthrough to sale ratio of their product or service. For instance, you may get a product that get 4% sales. That is, for every 100 visitors that visit the sales page, 4 actually go ahead to buy the product. This info is particularly useful if you are planning to use pay per click search engines to promote this product.
Do you have a control panel with which to check your stats and sales? This is usually a given with affiliate programs. A control panel encourages the affiliate to continue promoting the program as they can actually see how their promotions are performing. Therefore, it pays the merchant to ensure that there is a good selection of statistics available for those selling their products.
This is only a small selection of questions that should be asked before entering into any affiliate agreement - but certainly the most important ones. There are affiliate services set up to ensure that you make the right decisions and present you with the best offers. So if the decision making process becomes to difficult there are always alternatives.