Allan Gardyne is the founder and CEO of http://AssociatePrograms.com and a bunch of other affiliate-driven websites, including http://PayPerClickSearchEngines.com, http://KeywordWorkshop.com and http://LifetimeCommissions.com. A full-time affiliate marketer since 1998, he spends winters in Queensland, Australia, and summers in New Zealand. Top affiliates track what they're doing carefully and continually tweak things to see what produces the most sales. Here are tracking tools I recommend.
TOP TIP: AdSense Tracker
AdSense "channels" are useful for ads tracking, but they're seriously lacking if you want really helpful, detailed data. With AdSense Tracker, you can track every click-through on your AdSense ads to learn exactly what your visitors are looking for. When you have this data, it's easy to build more perfectly targeted, profitable pages. If you just have one small site, you probably don't need it. This is a tool for professionals.
Prolinkz
Prolinkz is a Perl script created by CGI wizard William Bontrager. You can use it to track clicks in ads in newsletters or on your website, to track responses from email newsletters. It can turn a long affiliate URL into a short one. It helps you quickly figure out which promotion was successful and which one wasn't. It's the tracking script we use at LifetimeCommissions.com. It's cheap and easy to install. Very useful.