@heskey: frag damage? No thank you... Against a light armored ship (high-tech ones) would be useful, but I guess that if your harmor has been stripped away the damage from the missile would nearly one-shot anything. That's beacuse to make some damage against even light armored cruisers you'd need a metric crapton of frag damage, but if the armor is not there for any reason... Well, all that damage would wreck anything.
What about a lot of EMP and some explosive damage? So if it hits a good part of your ship is offline and you have a nice hole in your armor, but if you manage to move it just hits your shields and does next to no damage. This could be an effective way of slowing down high-tech ships, and combining this missile with the burn drive low-tech ships could be very dangerous to high-tech ones. But the missile alone wouldn't be capable of murdering everything on its own. A cruiser armed with them and a lot of kinetic weaponry would be quite the challenge for any high-tech cruiser or even capital ship.
The idea sounds cool but would need to be balanced. Sure it'd be fun to launch phase missiles or phase torpedoes at someone but keep in mind they'll get launched at you too. Getting exploded can be fun if you learn from it but if you feel like you couldn't avoid it at all, it can be frustrating instead. 
So the question is, how would it be balanced? What would counter it? We need to make sure most if not all ships have some form of defense against this. Looking at your version of it, it seems like long range high damage PD would become mandatory (or just very good armor). In other words, any high tech ship not fielding a few burst PDs would be screwed.
Also, is that meant to be a weapon used only by phase ships? Because that could be part of what makes it balanced.
So what counter/defensive measure do you suggest?
Well, the simplest counter is to move, because the missile doesn't track the target while it's phased. So the weapon would be useless against anything smaller than a cruiser.
Then, the missile has average armor (maybe I forgot to say this...
), less than a reaper torpedo but more than a pilum, and is fairly slow so a single machine gun would not be enough to deal with it, but a pd laser or better weapons could destroy a lone missile. You'd need to use it when the pd is engaging something else, like some annihilator rockets.
I think that about everything bigger than a destroyer should have a good chance of evading or taking down a phase missile, especially true for high-tech (a couple of pd lasers or a burst laser combined with the agility of most high-tech ships are enough to avoid a lone missile) and low-tech (one flack or a couple of vulcans or mgs could be enough). Mid-tech would have some problems, as eagles and falcons usually have little to no point defense... But with their new maneuvering jets they would have the agility needed to avoid them.
Initially I thought of giving every ship the ability of using these missiles... But makes some sense that such weapon is used on a phase ship.
Maybe the phase ship could make the missile phase via some kind of device installed on the missile (like a "phase repeater" of some sort, that can use the energy from the ship's coils to phase a little portion of space around it, missile included). What do you think about this?
