Good affiliate tracking software must have following features: reliable tracking and real time statistics for you and your affiliates; anti-fraud protection; ability to track two-tier affiliate programs; easy integration with third party shopping cart systems.

Affiliate tracking software can be web-based (no installation of software required) and those that require installation on your site. For web based tracking software there are monthly hosting/maintenance fees.

AffiliateGuerilla

One of the few programs designed to run on Windows hosted websites.
The program comes with its own shopping cart and access database so there is no need to have separate shopping cart software.

Integrated with PayPal so that you can accept credit cards on your site without having a merchant account.

Program setup is easy via a web page interface. There is no need to setup cgi scripts. You simply upload your files to your Windows website or server and load setup.asp in your browser.

Set up to 5 levels of commissions per product. CPC program supported as well. Each affiliate can set up their own ad trackers.

Price: $89.

Also their offer quality ad tracking software for only $10.

For both products available free trials.

AffiliateShop

One of the most popular web-based affiliate tracking software that integrates with most third-party shopping cart systems.

Merchant can have a choice of a pay-per-click, pay-per-lead, pay-per-sale, pay-per-% of sale or pay-per-product quantity affiliate program model. Can track two-tier programs.

Allows merchants to export a Payment Report to PayPal's mass payment system.

Set up fee: $395.
Monthly Fee: $45.

AShop Software

Availbale 2 solutions:

AShop for Downloads is a complete solution for affiliate marketing and selling digital products online. Management of the store is all done through your browser. No special skills or knowledge are required. In addition, company provides exceptional support.

Requires a host server with PHP support, a mySQL database, and a compatible payment gateway service.
Gateway integration is included for AuthorizeNet, PayPal, 2CheckOut, WorldPay, PlanetPayment, PaySystems, and Manual Payment Processing.
Price: $200.

AShop Deluxe is an affiliate marketing system and shopping cart for selling tangible products.
Server requirements are the same.
Price: $230.

CyberTrakker

Cheap and reliable tracking software for advanced users. Perl CGI, HTML and JavaScript programming experience and tools are required to customize and install this system.Replicates a website for each new affiliate.
Generates HTML banner codes for each new affiliate.
Time, date, and IP address of each new affiliate sign up is recorded.
All the above is done instantly and automatically so your new affiliates can be selling for you right away.

You are responsible for integration, hosting and additional customization of the e-commerce shopping cart or integration with third party credit card processors.Price: $97.