There is no best. With so many systems you really need to think about your strategy and then pick one according to the type of solution you need and specific features.

As BEC said above, you usually don't start an affiliate program right away.

However, I disagree with BEC's reasoning that the branding and site need to be known. The real reason for waiting is so that you can refine your conversions and know where the best traffic is coming from.

Most big affiliates won't invest in you unless you have proven history/credibility and some objective conversion data.