I use Affiliate Future amongst numerous other networks, i do agree there are a few flaws to their backend systems, but their new interface is leaps and bounds better than the old interface but takes a little time getting used to if you've used the old system.
I have to say for ease of use Affiliate Window are good, as are Paidonresults.com (not a huge volume of merchants), DGM and Webgains are worth a mention too.
I have to say Buy.at would'nt rank highly on my list of favourite networks in terms of usability but they do have some fantastic brands on board so are hard to ignore.
A plus point for Affiliate Future is their huge range of merchants, literally huge and a merchant for nearly any concievable niche.
James a huge flaw i see with the AF interface is the lack of a decent search function, here are a few suggested improvements from a small affiliate like me.
a) its tucked away, put a link to a search function under the main menu of the merchant section.
b) it needs to offer a better broad match function - Ie. Unless you type in the direct name of the merchant you won't find it, an example being a search for lollipop does not show me the merchant Lollipop Animation
c) How about allowing people to search for anything contained in the merchants description, with so many merchants on offer it can be hard to find the right merchant for a niche. Ie. Let me search of animation and show me merchants like Lollipop Animation.