I created a script to do exactly this, it’s here: GitHub - deanbarrow/Affililink: A free way to automate your affiliate scheme. http://affililink.com/ · GitHub
It’ll add your affiliate tag to any Amazon link, and also rewrite other peoples with tags with your own.
It works on the client side so it’s just a case of adding a javascript file to your head section and configuring it.
It will do the same for eBay and can be setup to work with any affiliate scheme which uses a http://domain.com/?CODE=XYZ style linking structure.
I’ll be happy to answer any questions to help you get set up.