I'm planning on implementing three-way ball valves in my three vessel, single pump system and I want to be able to regulate flow on the outward side of the pump. Will a three-way ball valve effectively regulate the outward flow rate, or will it just divert flow in different directions, requiring two other one-way ball valves?
It depends on the configuration of the valve (two hole or three hole ball, allowed range of handle movement, etc). If it has an 'off' position, then you should be able to regulate the pump.
There are three hole balls are designed to blend the flow from two ports into one, and apparently don't shut off completely.
The two hole ones should have an off position, and should behave like a regular valve. I would assume that, if you get it from a brew shop it will be two hole, but it's always best to check it yourself.