Do you mean which script? or which aff/program? it's all depend on your niche, for goods use ebay , amazon, buy.com, and all the big known sites. ebay and amazon are when of the good aff program with helpful tools
If you meana content management system, then it'd be good to know just what kind of sites your'e trying to build. Are you looking to do datafeeds, online store, simple affiliate landing pages, etc? There are different solutions for different approaches. For a simple affiliate landing page, use simple a html page. lately I've taken to making a Squidoo lense featuring my aff product, and avoiding all the nonsense, also cashing in on Googles love affair with Squidoo.
Be sure to put it up at the top of the list. In fact do it while you're still thinking about which CMS to use And I'd go with Joomla!.
You need to be specific about what you asking, is it a affiliate script you after or just promoting affiliate products
I am currently using cj, shareasale and linkshare on my squidoo lenses. I have made some money with cj, but I am having the best luck so far with shareasale.
I agree, but I have been approved for some pretty good ones even though many did not accept my application.
I might not be the best person to give advice here, since I just started setting up my first affiliate site today, but I got Build a Niche Store (BANS) and it's a pretty neat program. Check out their website. It'll take some marketing skills to push that kind of a website, but it still seems like it's worth checking out.