An application domain is used to isolate applications so that they do not affect each other. Having a separate website for each service therefore offers higher fault-tolerance, and enables you to update only the changing service without affecting the others. However deployment will require a little more work. Also probably more resources will be consumed and initialization will take a little longer (since more application domains will be created), but if it's not a time or performance-critical application those may not be of much concern to you.
I think if there's a good separation between your services, your services have a (subjectively) reasonable complexity and the resulting overhead is negligible for you, it would be better to go for separate websites, otherwise not. (Yeah, in summary, it depends.)
Note: You might also want to take a look at this article:
Hosting multiple WCF services as one single service