I like to keep 4-7 "hunter" Lashers with safety overrides in my fleet even into the end game. It's a great expendable cloud of death you can hurl at things that like to skitter away, and you can use it to give yourself breathing room if you need to retreat.
In a good sized group (4-7) a pack of frigates that's receiving good, strategic, and frequent orders can be used to hunt down a carrier, break up a clustered enemy fleet, and move the battle to places you want it to be. It can be a bit demanding to keep an eye on them and make sure they don't run out of CR or start getting picked off, but it's worth it if you're okay with spending lots of command points and/or a few calculated losses.
If you're a power monger who believes in perfection, you could swap out the Lashers for Tempests, but I like my ships expendable.
You can also call in a frigate ball if you see an allied ship that needs help, but no one fast enough nearby to give them support. I'm usually much happier losing 2-3 Lashers, Brawlers, or Ceberi (Cerberuses, Cerberus'?) than I am with losing a Heron, Aurora, Legion, or any other important ship in my fleet. They usually make it in time to save a ship that's gone off chasing wolves and become outnumbered or trapped.
As an aside, can we make "off chasing wolves" a SS term that we all accept to mean "Making terrible decisions that get you and your allies killed?"
Frigates are great as late game reinforcements, and I feel like they have a place in large end game fleets as both chasers in pursuit scenarios and as mobile reinforcement if a battle is starting to go pear-shaped. For those reasons I keep on using frigates, even when I have several capital sized ships in my fleet.