I look more to functions, like the ability to do things like run campaigns, have good access to a lot of banners etc... NATS, especially if they have it set so you can see up to date conversion ratios for the site portfolio, is my favourite so far.

It has always amazed me how little effort some programs put into their affiliate areas, I know that they are meant for people in the know, etc... but some that I have seen would be downright embarrassing if i owned them. Others, have ridiculously slow navigation, and/or are devoid of what would be considered standard tools (CCBill stats, anyone?). I think that if you are using a program to represent yourself to the people who you are doing business with, it should kick ass.