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[Wyvern]

If i'm running mixed tech fleets my goto flagship is the Tartarus from shadowyards.

Neat!  Good to hear someone is having fun with that thing; I put together the code for its ship system, and that was... an interesting challenge.  (The game doesn't directly support changing the maximum shield arc; I had to cheat.)
As I recall, it doesn't actually boost shield efficiency by very much; the bigger benefit is typically reduced flux costs for firing energy weapons.  (And trying to balance that was a bit of a pain; the idea was to give just enough benefit that putting ballistic weapons into the omni slots wasn't a strictly superior choice.)

[JDCollie]

Vanilla ships. I often use the Aurora Class. It's handy, fast and doesn't need much supplies while it provides massive firepower and can be used against everything. Just destroyed a HSDF around 10 minutes ago, only testing because I don't want them to be my enemies.

Btw why is the Wolf frigate popular? Maybe I've tried bad builds but in my opinion frigates in general are weak and limited. It is too risky to use elite crew on such fragile platforms. Same thing with fighters.

The Wolf is a good mix of flexibility and firepower. It can mount decent weapons, has good shields, and has a phase skimmer.

Frigates have the advantage of diversified damage soaking. As long as your opponent can't immediately alpha down your shields, your frigates can duck in and out of the enemy's firing range, backing off to dump flux when they get close to overload. I keep around five frigates in my fleets right now at all times. I do occasionally lose one or two of them but it happens lot less often than you might think.

Sure, on their own frigates are weak, but if they are on their own you are using them wrong.

[RusMolot]

Native - Hyperion hands down.

I have two in my fleet, but only deploy one at a time, and always take control of it. I kitted it with a couple heavy blasters for massive alpha damage that quickly overloads most shields. It's got extended and stabilized shields with 20 capacitors, 10 flux vents, and resistant flux vents to soak up damage, and vent the flux faster. I'ts also got two tactical lasers, and an integrated targeting unit. The tactical lasers are more powerful than PD lasers, and I think longer range than LR PD lasers, so they help dish out the pain, but the ITU takes care of those pesky missiles that barely do damage to the shields (and are easy to avoid in the hyperion).

I support it with a couple Auroras, and an Apogee, they're mostly meat shields to keep the enemy fleet distracted while I pick it apart. I've also added a few Tempest frigates with unstable injectors and augmented engines to chase down running fighters and hounds (the Hyperion can chase them all down with a player at the helm, but the Tempest works better for the native AI). Together this fleet is enough to dominate the sector in native, no matter what I find.

PS. The most awesome part of the Hyperion is that it's completely energy based - I've been in some pretty long fights, and came out on top even when modules started failing due to long deployment because I used the shields to soak everything up, and vented when safe, then back into the fray.

[Midnight Kitsune]

...I've also added a few Tempest frigates with unstable injectors and augmented engines...

Is this supposed to be OR? Because you can't have both injectors and engines on the same bird...

[nonomo4]

Conquest, it has always been my favorite ship to fly with with its broadside kind of firepower rather than forward facing.

[Lolpingu]

Sajuuk-Khar.
It's the one of the only ships with the range and durability to take on several zorg cubes at once and live to tell the tale. The massive barrages of missiles that it is capable of can quickly dispatch any number of frigates, too.
The powerful pulsar beams that Hiigarans use as PD mean that fighters and missiles can't get close to it.
It kind of struggles with getting flanked by smaller ships, if the smaller ships have enough PD to repel the stream of missiles coming their way (which doesn't happen often, mind you)  However, with front shield emitter, the shield becomes 360 degrees. That, and you can put so many pulsar beams on it that it becomes dangerous to get into close range with this ship.
I also really like to helm Blackrock ships (particularly Nevermore and Karkinos) because of their massive burst damage. However, the fact that the AI can't handle flux properly means that they are no good as fleet ships. I'll usually give the Blackrocks a few prisoners to make sure that we're BFFs and then buy some ships from them to use myself while my fleet uses ships that are a bit more managable in long engagements.

[Midnight Kitsune]

Sajuuk-Khar.
It's the one of the only ships with the range and durability to take on several zorg cubes at once and live to tell the tale. The massive barrages of missiles that it is capable of can quickly dispatch any number of frigates, too.
The powerful pulsar beams that Hiigarans use as PD mean that fighters and missiles can't get close to it.
It kind of struggles with getting flanked by smaller ships, if the smaller ships have enough PD to repel the stream of missiles coming their way (which doesn't happen often, mind you)  However, with front shield emitter, the shield becomes 360 degrees. That, and you can put so many pulsar beams on it that it becomes dangerous to get into close range with this ship.

YAY! Another Khar lover!

[Lcu]

The Batavian Koning 

[06Elija]

In vanilla it's definitely the conquest. It blows up everything smaller than itself. I am only getting some trouble when I am trying to blow up a paragon, but otherwise incredible destruction potential.
Modded, I don't know yet. I only have recently discovered starsector and I am not too familiar with the ships included in some of the mods I have tried, but if I have a smaller fleet only made of frigates, I would take the Shadowyards enlil: incredible speed, superior maneuvrability and a steady flux managment make this ship my favourite.

[Erick Doe]

The Batavian Koning  

You know, just for that I've made you your own Koning.  

Spoiler

[close]

Just save it in the right folder and change its name to pb_battleship_koning

[Lcu]

The Batavian Koning  

You know, just for that I've made you your own Koning.  

Spoiler

[close]

Just save it in the right folder and change its name to pb_battleship_koning

Ooh, thanks!

[PsychoWolfen]

It used to be Onslaught but with the way how things are now with the new systems. It goes to the Dominator-class. Its the only other ship next to Apogee that has a large weapon slot within its class. I'm a sucker for ballistic weapons so strapping on a pair of Hephaestus Assault Guns or Mjolnir Cannons is so much fun with him.

[Sabaton]

It used to be Onslaught but with the way how things are now with the new systems. It goes to the Dominator-class. Its the only other ship next to Apogee that has a large weapon slot within its class. I'm a sucker for ballistic weapons so strapping on a pair of Hephaestus Assault Guns or Mjolnir Cannons is so much fun with him.

 I prefer needlers for shields and hellbores for armor. Add all the extra metal mods you can and you have a dominator that can bull rush a paragon and win.

[Schwartz]

The Tore Up Plenty mod has some nice, economical 2-deck carriers. The Lance is decent - if a bit unwieldy - and fields a HVD, the Rover can run 2 Double Flaks and 2 torpedoes. Easy to crack a tough nut with and then Flak away into their exposed hull. I know it's completely counter-intuitive, but most of the time I play my carriers as tacklers. They get Hardened Shields and decent flux reserves and then jump right into the thick of it, taking heat off the smaller ships. Sometimes this bites me in the ass, but a flux pool is too good a thing to waste sitting on the sidelines. They're not that difficult to get, which is why they're often my go-to ships for early and mid-game.

The next step up is the venerable Heron with PD Tactical Lasers and whatever medium gun complements your fleet. You get a much more sturdy ship with better stats for a Logistics point more.

The pinnacle of the 2-deck goodness would be the Charybdis from Shadowyards. It's probably too cheap with its 6 Logistics requirement, considering the crazy stats and energy weapon loadout you get.

[JDCollie]

I've recently become quite partial to the Shadowyards Tartarus. With siege mode ti makes a great spearhead against nearly everything but capitals, and is moderately fast (for a cruiser) when operating normally.