How do I use proton torpedoes?

Solution 1:

From http://www.swtor.com/community/showthread.php?p=1200623:

To fire a proton torpedo, position your cursor over the target and hold down the right mouse button until it establishes a lock. Your cursor must remain over the target the entire time. Once it's locked on, release the right mouse button to fire the proton torpedo.

This is different from regular missiles where you can just single click or drag over top without remaining over the target.

Edit: After obtaining and using them, I can verify that Killer's answer is also somewhat correct. They are only usable on "heavily shielded" targets: those that would normally take 4+ missiles (in the harder missions), such as the target on the bottom of space stations and all 5 shielded targets on Super Star Destroyers (or whatever the larger frigates are called). The shields on the smaller ships can't be targeted with the torpedoes.

Note that I said 5 above — Killer's assertion that there are never more than 4 targets you can use the torpedoes on is incorrect, especially since there is more than one ultra-ship in some missions. The (now deleted) answer he quotes was actually also correct — you can't use regular missiles on a heavily-shielded target unless (a) you are out of proton torpedoes or (b) you have fired a torpedo and it has not yet hit its target.

Solution 2:

Just Right Click.

Torpedos replace your standard missiles until exhausted. Because of the long lock-on >>delay, you may want to unequip the torpedoes entirely prior to some missions - they >>aren't great against fast-disappearing capital ships.

Absolutely wrong. Proton Torpedoes do NOT replace your standard missiles until they are done they are used in place of your regular missiles when attacking shielded targets and the mod does NOT have to be removed from mission to mission.

Correct, right click the shielded target (capital ship shield generators) until lock then release right click to fire HOWEVER you (currently as of patch 1.1) cannot fire regular missiles against these targets if you have Protons. However you have a max of 4 Protons and ALL MISSIONS that have the possibility of firing these Proton missiles have no more than the max of 4 targets to fire at.

Point in case is that having Proton missiles allows you to one shot shielded targets saving the time of wearing down these targets with lasers and missiles. Always useful.

TL;DR: Equip your proton missiles and use them 1 per target that allows it. Do not unequipt them for any reason (not necessary)