Here are some explanations:
Cookie Tracking
This method works by writing a small text file, a "cookie", to a user?s browser when they click on an affiliate link. This cookie holds the referring affiliate?s ID, which can be identified at the merchant?s order page to credit affiliates for referred sales.
Hit Counters
Where you use a small piece of script on every page like Sitemeter, extreme etc
CGI / URL Tracking
A Perl script or JavaScript which (1) reads the current URL, (2) grabs the affiliate ID, and appends it to the URL of the next page.
Other:
Any other method of tracking