Well... The biggest thing I built in ever would be the Starbases for the DC... although they are stations not Motherships.
...Though Fortress-Alpha is pretty maneuverable for a station due to ABH impulse thrusters, And it can still kill a lot of Collective Droneships at a time before taking crippling damage...
FUCK IT, IMMA PUT FORTRESS ALPHA HERE.
Don't let the stick-like structures fool you - they are full of guns and shields. (Meranera's legacy weps, ABH, Microtech and I think Archon's Plasma somewhere...)