The Artillery Beam is a main system which is unique to the Federation Cruisers that occupies a main room and cannot be manned. Once charged, it automatically fires a beam that pierces all shields (except the special Zoltan shield) and does one damage per room it hits. It also has the chance to start Fires. It can be upgraded to reduce firing interval. This weapon is incredibly deadly at higher levels. This is due to it doing widespread normal (system, hull, and crew) damage, and possibly causing fires to deal more system damage, and tie up enemy crew.
The Artillery Beam is great against the Rebel Flagship's first and second stages, as no defensive options either form has can stop a successful beam from dealing hull damage, and you are almost assured of system damage and fire damage. Against the third form, the Zoltan shield can block the damage and there is no point where the beam does good damage to the Zoltan shield. Once the shield is down, the beam returns to its effectiveness.
Unless you have a Clone Bay, when you board an enemy ship, you should consider switching the beam off by setting its energy to 0 bars, because an untimely blast can destroy the ship with your crew still on board. In addition, the random targeting of the beam means that it is unreliable for damaging any given system, and unlikely to destroy a system.
Mid to late game boarding is about targeting weapons systems to reduce hull damage and healing/clone bays to allow you to kill enemy crew. As a result, you are generally better served to put your beam power into your primary weapons sytem to give your boarding crew the reliable fire support they need to take the enemy ship. The only exception is if the artillery beam is the only way you have to damage systems, and you still have to destroy a clone/healing bay, at which point you may end up having to destroy the enemy ship to win the encounter, so consider your options.