It's all a matter of preference. I personally use KeyClone in conjunction with HotKeyNet. I plan to completely stop using KeyClone once I have my HKN script finished.

As far as I know, you can replicate most things that ISBoxer can do in either HKN or AutoHotkey if you take the time to learn the scripting. The only reason I don't use ISBoxer is because I don't want to pay another subscription on top of my multiple WoW subscriptions.