@Alex: here's an idea, stop me if you've had the same idea.
A weapon or system that would be mounted/installed on a specifically anti-phase ship, or phase-ship hunter if you will. This could take several forms, some way more cool than others.
First idea: "LOCK" - would be a sort of low-opacity beam with a special glow, and it would pass right through the normal universe (existing only in the alternate "phase" plane, if you follow) and thus all normal phase ships; but as soon as it touches a phase ship, it would have the effect of making the phase ship unable to phase back in, making the phase ship unable to stop building flux, until it reaches a forced flux overload; but it still wouldn't phase back in unless the lock is released by the phase hunter ship. It would then get to choose, tactically, the best time to let him phase back in. Say, when he's got a capital ship with all weapons trained on the spot 
Second idea: "PHASE DISRUPTOR" - a sort of EMP torpedo that would temporarily knockout the phase ship's ability to phase; but it would of course only be able to impact the phase ship if it was already phased in at the time of impact.
Hmm. That makes sense, but sounds like a "hard counter" to phase ships. It's tempting to have weapons like that - the Phase Beam and the Phase Charge Launcher were intended as something similar - but there are a few questions to ask here.
1. Are phase ships common enough to merit specific counters? That is, does it really make sense to have a ship dedicated to this, that's weaker in other circumstances?
2. Even if it does make sense as far as #1, what does it do to the battles where phase ships are involved? I suspect that might make them less interesting, since you'd just crush the enemy phase ships.
In general, I don't like the idea of having hard counters in the game - it reduces the impact of piloting skill. To top it off, any time there's one, the player can end up on the wrong end of it, too.
There are already so many ways to counter phasing - pressure by faster ships, pressure by Pilums (especially w/ ECCM), pressure by fighters, judicious burst fire, etc. If anything, phase ships are among the easier kills for the player already.
