We've tried most of them at one point or another...

We did have a very bad CJ experience, and have known others that have as well.
They owed us a couple thousand dollars and then didn't send the check... when we asked when they were going to send it they zeroed out our account and closed it that same day due to "non-activity." Since this happened I've encountered about a half dozen others that had the same thing happen to them. As you can imagine this was a real shock as they are one of the more highly branded affiliate processors.
Needless to say we'll now not sell anything for people using CJ which kind of bites as there are some people that we could seriously sell some stuff for but won't go near until they provide another processor option.

We found that Befree wasn't too bad unless you needed to get in touch with them - then they sucked. They don't return phone calls and rarely respond to email. This may have changed now that they're part of CJ but we've cut them off as well due to their new found 'CJ-ness'.

I've not heard anything bad about ClickBank, but they do need to work on their stats - or lack there of; I spoke to them recently and this is something they hope to have by fall.

Linkshare has been great to us; and if the merchants lag on sending payments, they deal with it right away.

I have to say though that after 5 years of having affiliate sites and selling stuff as an affiliate we've ultimately had the best experience with those people that do their own affiliate processing.
Sorry third party processors.