On one hand, long and ugly affiliate tracking links are a straight giveaway to people that you want to sell them a product (and people may be uncomfortable clicking on them). Therefore, making your link shorter and "nicer" looking will it give a more professional appearance. One of my favorite plugins for making links look "pretty" is the Pretty Links WordPress plugin.
Affiliate Marketplaces – ShareASale and ClickBank have thousands of merchants to choose from. It’s nice to login to 1 place and check the performance of multiple affiliates without going to each individual portal on each website. Many programs aren’t part of a marketplace though. I’m a big fan of ShareASale – there are so many companies and industries you can choose from.
Take ThirstyAffiliates, for example. This plugin helps you add affiliate links to your site and then organize and manage them. You can also include corresponding images, and track your links’ statistics. Pretty Links offers many of the same features, but focuses on optimizing your affiliate links. Both plugins have premium versions offering even more functionality. There are also plenty of alternative options to choose from.