The molecular Disruption Device, aka doctor device. Now that would be an interesting weapon to implement. Sort of an endgame doomsday scenario weapon, but it would also be cool to tone it down and have it as a just a planetary bombardment weapon or just highly effective against armored opponents and useless against shields. I haven't been able to play this game longer than 50 turns, so maybe there already exists a similar weapon, but I like the idea of it. Not just lasers and plasma and stuff.
You have siege driver for planetary bombardment in the mid/late game (if you get them of course)
Othre interesting late midgame/lategame weapons would be the Impactors, Morrigi grav cannon, the large ship missiles (Thud missile, Multywarhead Polaris missle, Blast beam missile, Blast storm missile), other interesting missiles (Kinetic missiles), or maybe antimatter cracker col (what better than to shoot an antimatter minefield towards your opponent :P), antimatter projectors, detonating antimatter torpedos, mesonic torpedos, ionic torpedos, kelvinic torpedos, or meson projectors :P
Or maybe something (even more) specialized like teh Damper beam (drains shields, energy weapons of the target reload longer, but does relatively little damage) or Heavy inertial cannons (not much damage, but slows targets) or Pulsed Graviton beam (can destroy turrets on the target easily, does some damage and act as a tractor beam) etc.