IR: Fast lock-on time, but flares will break their lock easily. Also, players generally have flares as their default countermeasure, so they will only have to press one button to deploy anti-IR countermeasures.
EM: Slower lock-on time, but chaff is slightly less likely to break the lock. Most importantly here: players will generally have to hit an additional key to switch to chaff in order to counter your EM missiles. This extra step makes it less likely for a player to counter your missile.
CS: Slowest lock-on time, but very difficult to break the lock. These missiles track the visual image of the enemy ship through a built-in camera. Chaff can break the lock, but (in my testing) only if the ship using chaff fires it while the missile is close. The best way for an enemy ship to defeat a CS missile is to hide behind something, since the CS missile will completely lose guidance if the target ship is not in line of sight. I think this is the best missile to use against players. The "missile launch" indicator for a CS missile is the same as the one for an EM missile, making the player think they can use chaff to defeat the missile... which usually doesn't work. Also, I don't think NPC pilots are capable of using countermeasures to defeat CS missiles.