1. Use Meta Refresh: A meta refresh is a simple bit of HTML code which automatically redirects your visitor to another page (your affiliate URL). It provides a neat way of presenting affiliate links in newsletters. It probably helps reduce commission bypassing and commission hijacking. A big advantage of using meta refreshes is that if merchants change their affiliate links, you can change links on dozens of pages quickly and easily by altering only one file.
One problem is that some search engines don't like meta refreshes because they're frequently used for unsavory purposes. So if you use this technique, use it with caution.
2. Use a URL redirection service. You can use free services or buy a unique domain name for each affiliate program you join. URL redirection makes affiliate links less obvious, so this will reduce some commission thefts.
3. Use a web-based ad tracking service. The ad tracking link initially hides the affiliate link, reducing thefts.
4. Use an ad tracking script. Good ad tracking scripts hide the affiliate link as well as being useful for tracking. It has the advantage that it doesn't promote someone else's domain.
Be aware that thievery is a problem for online businesses and take the necessary steps to protect your commissions.