Finally after a long time, The Hidden Affiliate Links plugin for WordPress 3.0.1 is here.
The previous version stopped working a long time ago when wordpress 2.5 was released ( yes it's really that long ago ).
I tested the current version on WordPress 3.0.1. It might work on older versions but I don't plan to support them.
The download, install and usage instructions are on the plugin's page.
I tried to host this plugin on the official wordpress plugins repository so you could see update notifications right in wordpres admin but apparently someone there doesn't like the fact that this plugin hides links so it was not accepted.
I think this is wrong because there are other plugins there that can somehow hide links ( like the redirection plugin ) and even without a plugin if someone wants to hide a link they can still do it easily by using any url shortner.
Anyway the idea is if you want to be notified about updates make sure you subscribe to my RSS feed.
Feel free to ask any questions about this plugin in the comments.