What Sven said.
Never use heatseekers unless you know there are no friendlies around. Heatseekers (missile/missile) are just as happy to target trade ships and your allies as they are to target pirates, and you have zero control over what they target. That said, most of my ships use heatseekers because I otherwise suck worse than the easy AI at hitting things.
Sniper missiles (missile/beam) are by far the ideal missile but I find them very difficult to target properly. My solution is to build them into turrets and let the AI target them. Because they are seeking weapons, they do not suffer from the usually atrocious hit chance of AIs, and this makes them ideal for offensive turrets, if you are going to have offensive turrets.
With missiles, and especially if you are using sniper missiles, be extremely vigilant in how many modules you use, your power system regeneration capacity and your power storage capacity. Sniper missiles require roughly two power capacitors for each missile and beam module (plus any tertiary effect module). Especially if you are using sniper missiles in AI controlled turrets, if you do not have adequate power generation and storage, they will leave you dead in space without power for anything else.
Build your power system first, make it as powerful as you can. Then add as many capacitors as necessary to absorb all the power your power system can generate for 45 seconds. Add as many shield regenerators as you are likely to have on your finished ship as well as any defensive effect systems. Take your ship out for a short test drive before adding weapons. Turn on all systems and push your engines to the max. See how much energy you are using and subtract that from the total power your ship generates. Multiply that remainder by 45 and then divide by 2250 to get a rough idea of the maximum amount of modules you can put into your sniper missile systems.
We wary however of groupings. The more separate missiles fired by any single computer set (this goes for any weapon), the more power they use, going up by 10% for each weapon system added. For the least power usage, have only one missile per computer set. That said, point defense systems could make your ship unable to hit anything due to your few missiles being shot down. On a server with the AI set to easy, point defense is so ineffective that you can probably get away with just having a couple of super missiles. The higher the AI difficulty, the more effective point defense becomes, and the more necessary it is to have multiple launchers despite the higher energy cost so as to saturate point defense and still get adequate missile hits.
I generally prefer ion for tertiary effect. Explosive will greatly magnify the destructive effect of your missiles, 'only' if your target's shields are down. I find however that once shields are down, missiles will make short work of their target regardless of whether or not they have extra explosive effect. Moreover, missiles using explosive effect are likely to have full explosive effect ratios, whereas with ion for tertiary effect, however many or few ion effect modules you use will be just as useful. That means ultimately bigger missiles and significantly better utility for taking down shields. The bigger your missiles, the more ion effect you can afford to put on missiles. Do not add ion effect to small missiles, as you don't want to reduce the block damage of a missile to the point where it is not punching it's maximum possible holes in targets.
If you are building ships to use missiles, expect to do fiddling with your systems while you iron out the kinks and ratios. Test early, test often. If you intend to build a highly detailed and intricate ship, consider building a battle cube (or similar rough assemblage of blocks) to start with just to be certain of the ratios of systems. Make that work flawlessly then deconstruct that and build the true ship, confident that the systems will function properly together.
