This post contains affiliate links.
I realized just yesterday that WP-Hypnolinks was shut down and no longer officially exists, I had been using this plugin for over a year to do all my affiliate linking on blog posts on several of my sites. This was a great alternative to Pretty Link Pro, Ninja Affiliate and was lightning fast at rendering a large number of links with a lot of flexibility.
I augmented it with the LinkSmart program which goes above and beyond just simply creating affiliate links, LinkSmart which I did a review on back in June 2013 is basically a full cloud based linker that finds your most common keywords, tracks clicks, impressions and even allows for dynamic keyword changes and uploads on the fly.
Read my review of LinkSmart on DragonBlogger here: http://www.dragonblogger.com/linksmart-wordpress-integration-for-analytics-and-affiliate-marketing/
They also have the marketplace coming which once in place gives advertisers the ability to purchase some link advertising on your site by targeting your best keywords. This also is Google ToS compliant because there are no dofollow links for advertisers, in fact there are no links recorded in the HTML source code at all. The links are rendered after the page is loaded on the browser and all content is served from the cloud which does not put strain on your hosting provider or database which is something most WordPress plugins do to track link clicks and such.
Anyway, I haven’t transitioned off of WP-Hypnolinks yet, but Pretty Link Pro is awesome and recommended. LinkSmart is fantastic but has one drawback in that you can’t disable it for specific posts, I need this functionality because when you do sponsored posts you don’t want your affiliate links competing with your sponsored links or advertisers content. Pretty Link Pro allows you to disable on specific posts which makes it advertiser and sponsor friendly.