I don't think there's much I could add to this thread other than briefly repeating what's already been described to work for anti-phase Ship tactics:
1) Beam weapons are your friend, especially Ion Beam, Tachyon Lance and High Intensity Laser. Massed Taclasers and Grav beams also help somewhat.
2) A harbinger on your side (preferrably with an officer that has Elite Phase Mastery, Elite Target Anlysis, Helsmanship, Systems Expertise, Reliability Engineering and a choice between gunnery implants or energy weapon mastery) will hardcounter enemy phase ships. They work incredibly well under AI control with 3 Alternating Antimatter Blasters + ITU + Unstable Injector. Variants also making use of the Ion Pulser and Ion Beams with the same hullmods will either entirely immobilize enemy phase ships for your allies to butcher them or will do it themselves. Expanded Magazines is also a good hullmod to install if the weapons synergize.
3)Warthogs with the Fighter Uplink Commander Skill also go fast enough to keep up with most phase ships, and they hurt. Not recommended against dooms
4)fast ships with 360 shields will harass and distract/take down phase ships, even the doom if properly S-modded and kitted out. medium to fast Destroyers like the Sunder or the Hammerhead do the job almost slawlessly with both Safety Overrides and Extended shields.
5)heavy long range missile firepower also makes it really, really hard for most phaseships to approach a target. This is one of the only things ECCM+Elite Missile Specialization Pilum/Salamander spam is very good at. Missile-focus ships firing limited ammunition ordnance also help, any phaseship approaching an enemy that has a Gryphon loaded to the brim with ECCM'd Harpoons and gets high on flux is going to be threading the needle more than it will ever want to.
You don't really need to follow all of them at once, having a good rapresentation of 2 or even just one of the above "concepts" across your fleet is going to put you in a very good spot against the Phase Weebs when encountering enemies making significant use of phase ships.