Just off the top of my head. You might have several of these in a late game fleet, so you might use several of them at once.
Progenitor Monthership + Iconus Guardian - Greatly increases the durability of an Advent fleet, you should have this in every fleet. Well managed use of it can allow you to tank Missile barrage and other painful abilities. Weak to phase missiles however as they go through shields.
Radiance Battleship + Progenitor Mothership + Rapture Battlecruiser(AKA Holy Trinity) - There are a couple of variations to this, and its not as popular as it used to be, but you need at least two of the three ships. The ideal setup is for the Rapture to cast vengeance on the Radiance, which uses animosity to draw enemy fire while the Mothership casts malice. This not only causes Vengeance to do a lot of damage to enemy ships attacking the Raidance but malice will further enhance it. Add Cleansing Brilliance on the Radiance and it can theoretically do a lot of damage.
In practice it doesn't work so great because animosity is bugged so that new attack orders will override it (though if your friend doesn't know that its still good, alternatively convince him to play with the Project Equilibrium balance mod where it is fixed), and you need a high level mothership to keep both shield restore and malice up. Still worth it to use some of these tricks though if you happen to have these ships out anyways.
Halycon Carrier + Illums/Desdras - More obvious one, this one just seeks to maximize DPS with amplify energy aurora. Not as good now that Illums have been fixed, but you should always have a Halycon anyways and if you aren't facing a lot of strikecraft its a good ability to invest in.
Halycon + Rapture + Carrier Cruisers - If your opponent leaves him self open to strike craft, use this. Halycon gets extra squadrons with a large buff with anima tempest, the carrier cruisers provide most of your drones while the Rapture amplifies the damage they do. Best of all you can park these on the other side of the gravity well while your strikecraft get the benefits and destroy the enemy fleet.
Level 6 Progenitor + Dead Capital Ships - Not really a synergy, but the Progens lvl 6 ability is seriously under utilized if the game lasts long enough to get one. Your level 8 Halycon dies? Build a new one and cast resurrection on it. New level 8 Halycon. Basically makes even high level caps expendable as long as you have one level 6 Progen and can afford to keep replacing Capital ships. Also makes the rest of these synergies much easier as you can maintain the high level capital ships to really exploit them.