Mines - Scout(must have to use ability to detect mines) and Flak Frigates do the job easily.
In Rebellion actually the scouts clear mine ability is passive. Simply bringing a scout near a minefield is enough to make them vulnerable to weapons.
I usually have flak frigates or my titan close to the scout while clearing mines, since these units can fire in all direction, and even better the titan can engage multiple targets.
The Advent loyalists also have a cool ability on their carrier you can research that lets them take over enemy minefields.
Second, super weapons. Under circumstances where it's simply not possible to get to the enemy world that's using them for some time, what's the best way to deal with these? Planetary shields help with novaliths if you happen to be TEC, but do the other races have any options beyond "constantly getting your homeworld flattened?"
The only superweapon that can inflict damage to a planet is the TEC's Novalith cannon, and this can be pretty much countered by building a starbase at your important planets and getting the "Auxiliary Government" or equivalent upgrades. This upgrade makes it impossible to lose a planet to enemy bombardment, including Novaliths, as long as the Starbase is still alive.
You still may want to build shield generators as TEC though, as Auxiliary Government does nothing to reduce the number of people killed by a Novalith, but shield generators do.