Maybe all the end-weapon techs can give access to a Superweapon Module. Each module would cost 1000 mp points (Hyper-Atomic Magnetic Acceleration Tracks are expensive) and take up 100 space points (that Core-Powered Fusion Discombobulator is quite large), but grant super-destructive abilities. The space and cost requirements generally mean that to get one, you must have researched far up the advanced hulls and miniturization tech tree before you can implement one of these modules. These modules also mean that the ships will be very expensive and have a very limited function. They could be:
Black Hole Chaingun: A device that generates and fires mini-black holes very rapidly. These black holes eat through the hull of the ship or starbase, distort any surviving wreckage past salvage with super-gravital effects, and kill all lifeforms within 100 meters of the line of impact (yes, a line - the black holes will not stop and do so much damage that it can only be called that). It destroys every ship in one hit; defenses are rendered uselss, as nothing can really stop a black hole traveling at Mach 50. There is a catch to an infinite attack value: it can only fire once every 3 firing turns, making it very vulnearable to fleets.
Targeted Ionizing Sphere: A module that compresses a beam of energy and then redirects it at a planet. The energy beam cuts through the crust and mantle of the target planet and strikes the core, where it superheats the inner core of the planet, which then expands outward and splits the planet along ionized boundaries. The result is that the planet is destroyed, of course; there is a 50% chance that the superheated magma will instead find a way onto the surface ( \_/ Muahahahaha >) ) in which case supervolcanic eruptions will occur, wiping out 5-10 billion people, decreasing planet quality 50-100%, and taking out 90% of the planetary infrastructure.
Dark Matter Hairpin Cloak: A projectile that contains extremely compressed (10 to the negative 200th power, in terms of before-and-after size comparisons) dark matter. It is launched at a star; once the missle gets too close to the chromosphere to maintain system integrity, it splits in half widthwise; the dark matter that was compressed inside the projectile (the projectile is itself the size of a city block, and contains a massive cargo hold and a hyperspace drive) expands outward at a macrocosmic rate, engulfing the star in a cloak of darkness. The dark matter 'cools off' the star by disrupting the nuclear fusion cycle; the velocity of the original projectile, transferred to the dark matter, transferred to the star, usually is enough to collapse the superstructure and dissipate the gases. The result is a swirling miasma of gas and dark matter; colonies around the star can find other ways to gather the necessary energy to survive, like geothermal steam, but suffer a major planetary quality loss (on the order of 50-100%), lose all farms and the ability to create farms, and take on a morale loss of 20%. This means it can be prudent to close down colonies that once orbited the star. The device kills off life on uncolonized worlds that don't have advanced beings to regulate the ecology; all uncolonized, habitable worlds in that system become uninhabitable. There is a 50% chance that the missle will detonate immaturely, in which case the dark matter will trigger a solar flare that destroys all ships in a 2-tile radius, including the ship that launched the missle.
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but if that will happen, it should have a high research to attain
that! to balance your galactic powers.. right ? 
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