Setting up your links to be and look professional and then with some way to measure and track your results is the best way to go, most people fail to use the right type of affiliate links because that either don't know how to use professional links or they think it's quicker just to use a standard affiliate link.
So the key to setting up better looking affiliate links is with a a link redirect, these are either html or php based and are very easy to implement, html redirects are done through having your own domain name and placing a small snippet of code where you need to and it will redirect through your affiliate link smoothly, without actually exposing your affiliate link, or there are php redirect software that will save a file that is uploaded to your website and make the file hide your affiliate link, like it's part of your website.
There are other html encryption methods out there too and they are free to use, just Google it and you will recieve.
A good redirect software hides your affiliate link so no other spyware software can erase your affiliate link for the spyware user to replace with their own affiliate link and steal your commissions.
Although link re-directs are not a good thing for the search engines as they seem to penalize them, they are excellent for newsletters and email autoresponder messages as they appear professional and include the domain name of your site within the url.