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[SCC]

Hyperion is a pretty viable choice with wolfpack tactics. If it was a flagship skill, it would be one of the better ones (even if pretty limited), though mostly because Hyperion is good enough to be viable even in the endgame. Teleport to anything that seems vulnerable, duel it, then teleport away, vent and repeat.

[Megas]

Overpowered hero unit that can do everything, or at least the role that makes things dead fast.  Bonus points if it is unique enough to be a signature ship.  So far, the closest ship to that role is the Ziggurat (powerful and one-of-a-kind).  Problem with Z is it is a massive hangar queen ill-suited for chain-battling, and has trouble targeting station modules.  Also cannot do stealth ops with it in core worlds because its one-of-a-kind nature identifies your fleet.

[Deshara]

light, manueverable, effectively incapable of fighting anything its size class or up with its gun(s?)

I've seen people using frigates to solo capitals and even starbases(helmut is godly with a HyperionExcelsior), but I just don't have the patience and skill to do that. I usually fly the biggest or one of the biggest ships I can get simply because it allows me to make mistakes without getting oneshotted by a rando torpedo.

I spent several hours trying to kill a station with my whole maxed-out DP fleet, then slapped 2 small reapers & 2 medium reapers onto a medusa with EMR (not sure which mod gave me a medusa that can mount missiles on the mediums but thats definitely not vanilla) with 2 IR lasers & a wing of broadswords & pulverized the station nearly single-handedly. my 40 reaper medusa is a monster

[TaLaR]

Chain-deployed AM Afflictors. Nothing comes close in terms of in-game resource cost-efficiency, but is real-time consuming. This does become stale after a while, so I took a break from the game until next update.

[Killian]

I'd like to try a dedicated missile spammer but it seems like even the modders shy away from making something that vomits a million missiles across the map.

Grab the Hiigaran Descendents, get yourself a Kuun-Lan Battlecruiser or Vanaar Cruiser, and fit them out with Abas missiles - they automatically reload over time, and the Kuun-Lan's active ability significantly reduces missile reload times (the Vanaar just has flares). Catch is the Kuun-Lan's system generates unhealthy amounts of flux and Abas TAMs are energy damage so they're not particularly good against anything (having another ship to drop the target's shields with kinetics and then using HE missiles is far faster for kills), though they aren't particularly bad against anything either.

Still, if you push it to the limit with skills and/or a couple of good officers you can have dozens of missiles flying at a time, which is fun.

Alternately the ARS/Legacy of Arkgneisis Donovan-class hull has a Missile Autoforge which can replenish any missile system, but disables weapons whilst active and likewise generates a lot of flux. Eight small missile mounts makes for quite a bit of missile spam.

[Daynen]

Glue 2-3 Atlas MK IIs together. By the dawn's early light, there will be nothing left to be seen!

I LIKE THE WAY YOU THINK

[Wyvern]

Personally I trend towards fast cruisers (or occasionally battlecruisers, though none of the vanilla options there are really to my taste).

Quick enough to get where it needs to be, durable enough that I'm not one mistake away from blowing up, and with enough firepower to make a difference wherever I put it.

From vanilla, this usually means an Aurora or Fury.

[Null Ganymede]

High mobility to reinforce wherever needed.

That's not necessarily Safety Overrides or a phase ship though. Low-tech capitals with Burn Drive and an Auxiliary Thrusters mod are extremely mobile, and technically a dedicated carrier flagship could fill the same role though I haven't tried it yet.

[Undead]

The best flagship is a mudskipper mk2 with operations center 

[shoi]

Higher end frigate or destroyer. In my vanilla run I started with a wolf and played through the rest using a hyperion.

There are a few bigger ships that would fit my playstyle but generally I don't use Cruisers and up because i play pretty aggresively, which more often than not leads to me overextending in them and dying

[ElPresidente]

I'd like to try a dedicated missile spammer but it seems like even the modders shy away from making something that vomits a million missiles across the map.

There is one modded ships called the Macross that fits your bill.
Also, I think the Interstellar Imperium had a MASSIVE MIRV missile launcher ship + alahu akbar varant.

[savvygui]

Capital: It just has to be fast. In vanilla I try to fly an Odyssey as much as possible and often wind up flying one in modded runs, too, though I like battlecruisers in general. I let my fleet hold a battle line and try to pick off stragglers on the flanks or reinforce the line where needed.

Cruiser: Brawler. Speed is a nice bonus, but I prioritize hang time in a fight (usually with a good shield and flux stats). Aurora/Fury are my vanilla choices for this; shout out to Shadowyards' Charybdis, though. I run SO cruisers sometimes, but being stuck at 450 range on a cruiser-size hull is painful.

Destroyer: SO. Pretty much just the default SO Hammerhead build in vanilla until I build up a better fleet — destroyers are my least-flown ships by far. That may change: I've been keeping two SO Magellan Capellas in my current modded fleet both as AI hunter/killers and as backup flagships, and woah boy, they are terrifying.

Frig: Superfrigate. The closer I can get to playing a bullet hell shmup, the better.