Ok missiles totally baffled me at first. Go to the ship design thread and find my Snake Missile thread.
In short, when you design missiles, you have WARHEAD, ENGINES, FUEL, and AGILITY.
Don't worry about the rest, or that multistage stuff. You'll get there eventually. I'm not there yet.
Each interger you put in those boxes is 1 missile size point, or MSP.
So if from the list above, you put 0.25 in each of the boxes, you'll have a 1 MSP missile.
Now heres where I was really confused-- Just because you put a "1" in the warhead, that doesnt give you a "Warhead: 1" missile. Your warhead technology improves Warhead value per MSP, so a more advanced warhead tech will give you a bigger "Warhead" value for the same amount of MSP. Confused yet?
Early on your tech will be smege. So don't worry about it too much. From that snake missile thread, you can see that i had Hullspace and Missile Size confused for my first run, so I made an enormous missile that was totally pointless.
However, on the second page, my anti-missile-missle (highly agile, short range) is pretty good.
You want your anti ship missiles, size 6 or size 4, to have reasonable range (~100 m km) and get there reasonably fast (30km/s) with some wiggle room in both directions. Once you get your missle pretty much set up, you can dink up the agility and dink down the engine speed to improve the to hit. I'm going after really fast aliens in my current game, their slow ships go 9km/s, so my missiles need good "to hit ratings"