I use a custom lesson-booking and payments system on my site, so 'Joomla That!' had to do some bespoke development to integrate this with their off-the-shelf plugin. They did this very quickly and communicated with me throughout the work. Prices and so on were upfront and honest; in my opinion anyone has been 'burnt' before by custom developers should have no concerns about approaching them for this kind of integration. The service and support was absolutely exemplary.
I also had a couple of questions at the end and one styling issue which were resolved very quickly.
I think this extension does everything you could expect from an affiliates system. One thing I'd love to see would be the ability to create a kind-of gallery for banner images, so affiliates could browse through and then copy-paste a snippet of code that would include their individual link. As it is, affiliates are simply provided with an individual URL that they can use however they wish. I suppose that maximises flexibility and keeps it simple.
You can pay affiliates a percentage or a set rate, but as far as I can tell you can't change the rate depending on the product that was sold or the overall price of the sale. That's not something I need but there might be people out there who'd need something like that - their profit margins could differ between products or they might want affiliates to push particular items so could offer better commissions. Apologies if that is actually in there - I have a tendency to skim read...
So overall, Affiliate Tracker provides an excellent way to promote your site with very low upfront costs. I expect it to become one of the most popular extensions in the Joomla directory. The support was probably the best I've experienced, too.