I have been testing out 2 affiliate systems for a Joomla website.
idevaffiliate and VMAffiliate
idevaffiliate is the bigger and more expensive of the 2 options with prices ranging up to $300 for the gold edition.
It requires its own unique database and has a load of options. however the default affiliate link will only link to the front page of the site.
you can add other pages but these have to be done individually by the administrator and then the affiliate has to generate unique linking code using the backend system before they can link to individual prodict pages, and only pages that the admin has specified in the idev admin panel.
It has the ability to have 2 tier affiliates (eg you refer another affiliate and you get 10% of whatever they make) and it has the option to have multiple cost levels.
Eg, you make 10% unless you do more than $5000 in sales, then you get 15%
It also has tracking and logging for affiliates to log in and check how many visitors they have sent to you and how many have converted.
Then there is VM affiliate, it has no 2nd tier affiliate capability, and you can only specify one default flat rate for the affiliates, but it integrates very easily into virtuemart, uses the existing virtuemart database, it also generates links for everything in your shop in the backend for the affiliate to use.
The tracking it a lot more basic but its only $80 and its a lot simpler.
You can have a play with both and let me know what you think.
Note, I have only added a few dozen products in idev, but if you like it I will add more.
Ps, nothing is set in stone at the moment, I am still testing