Monitoring your progress by tracking sales activity is an essential part of affiliate marketing. Any affiliate program should at a minimum be able to provide you with basic reports on sales you've made. Be extremely cautious of any program that does not provide sales reports to affiliates.
If the merchant cannot supply even basic reporting, it's difficult to be confident that sales are correctly logged, or even worse, that they are not actively deceiving their affiliates (sadly, it does happen).
Commission Junction, BeFree and LinkShare are the three largest companies that host affiliate programs for many different vendors. All have generally good reputations (none are perfect) and provide reasonably detailed reporting for all their merchants. The online payment processor, ClickBank is another major third party affiliate program manager, although its reporting is very basic in comparison with the other three above.
Whilst perhaps not absolutely essential, it will benefit you greatly if the affiliate program provides detailed statistics on your sales and referral activity. The more detail, the better.
Two features to look out for are referring pages stats and the ability to add your own ad tracking codes to links.
The former will tell you what page the visitor was on when they clicked on your affiliate link. The latter enables you to create unique URL's for use in different locations, providing you with independent stats for each.
Unfortunately, for various reasons recording the referring page doesn't always work. For example, if the visitor used a bookmark, there will be no referring page to record, or if the affiliate employs redirect scripts or URL cloaking the referring URL shown in your stats will usually be the URL of the script itself.
Ad tracking code is far more useful because it provides the ability to analyze the click-through to sales ratios for different links or banners in specific locations.
This enables you to see what works best and gradually fine tune your promotions for maximum effectiveness.
PushButtonPublishing is an example of an affiliate program that provides individual ad tracking. For every single link you create, you can set up an ad campaign with your own written description tied to a unique 4 digit ad ID in your referral URL. This enables you to quickly and easily evaluate and compare the performance of links in different locations.
Next to consider is the affiliate program's terms and conditions