John,
The industry certainly needs to get off of the cookie based 1x1 pixel tracking method but there has yet to be an alternative. Studies predict that 30-50% of cookies are blocked or deleted. The best tracking I have seen is from Post Affiliate Pro as they use session cookies, standard third party cookies and flash cookies. They require that you add a javascript on every page which can be done conditionally so its not popping off unless for affiliate tracking. Its dirty cheap but not for very large programs.
One suggestion is to find out how Visa handles their transactions as to my knowledge they are flawless.
If anyone has a bullet proof solution I am all ears.
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