There have been a number of one-off aircraft which attached one plane's cockpit to another aircraft for testing or training purposes. Furthermore, if your restriction of "proper" flight controls were lifted we could consider a number of bombers which were "flown" by the bombardier, by redundant interfaces to the autopilot system.
There is also the unique situation of lifting bodies and attached gliders. These were technically three or more people in control of two or more aircraft. Given that the child aircraft would need to be trimmed in order to avoid upsetting flight, input to control surfaces by 3 or more people could influence the flight path of the agglomerated system.
The only "production" aircraft I can think of with more than two sets of flight controls is White Knight Two which has a complete cockpit in each of its two fuselages. Unfortunately I cannot find an indication as to whether all four sets of controls can assert authority at the same time. If so, and if Space Ship Two's controls are not locked out while it is being carried there would actually be six people influencing the flight of the aircraft in some way.