Creating an affiliate program - Commission Junction? Linkshare?

Anyone ever work with Commission Junction or Linkshare (or others) as an advertiser? I'm looking to set up an affiliate program for my marketplace app. We have the technical skill to implement an affiliate program ourselves, but I'm curious about peoples' experiences with some of the larger organizations.

Specifically, how easy are they to interface with? Is it smooth and easy (ie. REST APIs, RSS/Atom feeds, etc.) or clunky and crappy (FTP'ing files, proprietary formats).

Also, on the publisher side, which do you prefer to work with, and why?

Update : I heard back from CJ and they want $9k down. I'll cross them off my list...

I worked with Specific Media previously and had good success with them. They seemed to be real honest in their recommendations, worked closely with me to tune my program as we learned more and more about the response and were generous when a couple of affiliates tried to 'play' my promotion and screw me. They were economical in getting started too, no big initial payment, at least when I worked with them.

Best success.

If you expect to be pretty big, you'll probably end up working with all of the above - regardless of how much easier to work with one is over the other. But all in all, I do recommend using them. However, once you grow to a certain size, you can expect to dedicate one employee entirely on affiliate management.

You are going to pay an arm and a leg both in upfront costs and a percentage of your payouts to affiliates (20-30%).

If you have the capability to do this yourself, you should definitely do so.

I checked out your site - very nice! If you are interested in setting up a custom affiliate program, feel free to ping me -- we are in beta and looking for feedback!

We have used Shareasale and the Google Affiliate Network. Shareasale is fine (with pretty reasonable startup costs) and the GAN is OK. They could use a lot of work on it though.