[narf poit chez BOOM]

The acceleration for X will be cos(theta) times the ship's engine power, while the acceleration for Y will be sin(theta) times the engine power.

And theta will be the direction to accelerate in.

Got that far. It's the whole 'How do I calculate theta' that's the problem.

S1x-S2x = (V1x-V2x) * T + ((A1*cos(Theta)) -A2x) * T * T

V1x would be Enemy Velocity X, A1 would be Acceleration Vector Length, Theta would be the angle to accelerate in, A2x would be Target Acceleration X and T would be Time?
What are S1 and S2?

Unknowns are Theta and T, common to both.
You can rearrange the first formula to get Theta = F(T)... there will be inverse cos or inverse sin in it.
Replace the Theta in the second equation with F(T).

What is 'F'?

Now you've got a big horrid, fearsome beasty with only T as an unknown. Solve for T. You'll probably need a big sheet of paper, or maybe maple to simplify it down to a one-line equation to code in.
Now I'm wondering which variation of that formula you gave I should use to figure out T or Theta or whatever it's supposed to give me.
Plus, I think that 'Big sheet of paper' part may put it somewhat outside my mathematical ability.

Plug T into the first formula again, and Solve for Theta.

Your ship/missile can then accelerate in the direction of Theta for time T. (Theta = 0 means the +X direction, 90 degrees = +Y)
Yeah, I may need a bit of help to figure out exactly how to do that.

Going to have to fiddle with the angle, then. C# uses radians for 3d object angles and 0 is +Y (Although I'm using X and Z for horizontal and vertical).

@Jack: That formula you gave me gives Time, right?

I'll go let my brain collapse for a while, then come back and see if I can figure this out. If brute force can figure it out, then I may be able to turtle my way through before my brain starts screaming at me.