It also depends on the niche you are in.

The commission hijacking Rob mentioned is more prevalent in Internet marketing niche, since the subscribers of a JV partner are more likely to be savvy enough to replace the JV guy's CB hoplink with their own so the subscriber gets the commission...

However, as I understand CB recently introduced a white list feature where only allowed affiliates can promote a product which is ideal for a JV launch. 8)

Given this, Clickbank also has many other advantages like being a third party affiliate tracker which gives some impartiality. An in house affiliate system is more easily accused of shaving as well since most of the time you host the mysql tables and can easily go in and change some values here and there...

With Clickbank you can save an accounting department, since they take care of that for your affiliates, with wiring all the money keeping the tab etc etc.

Given all this, I plan on using Clickbank all the way