I've been researching the available controllers for about a year as I was going to upgrade my ACII last Christmas...but got laid off in November so never did.
It COMPLETELY depends on what you will want to do now and in the future. Most disagreements come from the value/functionality arguments, followed by reliability.
The value/functionality arguments for more expensive controllers becomes irrelevant if you'll never use that functionality...for instance Tunze Control. Profilux Users love to use this as a reason why that controller is really cost competitive after all...but if you have lots of equipment to control (i.e. outlets to control that controller gets expensive fast).
If you want to be able to program/control through the internet then you'll want to look at the APEX or Profilux.
If you want to only monitor or get email alerts to a problem then the Reefkeeper Elite or APEX will work fine for less $$$.
If you don't need complex control then Reefkeeper Lite or ACJr would do.
As far as Neptune Systems (ACJR, AC3, Apex) goes....Curt is fantastic at supporting his users and will personally help you with questions. As I said, I have an AC2 and I have never had a problem with it. I can't imagine not having a controller on my system.
I use mine for lighting main tank, refugium, and frag tank, Kalk ATO (overide if pH too high), Kalk stirrer, cooling/heating, dosing, and Ozone.