
Autofire is a great tool and should be used in most cases. The simple reason behind this is that human reflexes are slow. If you wait until you see the weapon charge/lock-on bar turn green, then pause the game - you've wasted a few tenths of a second. Over the course of a battle this adds up to a few extra seconds you've "given away" (to the enemy AI, which has none of these limitations). Consistently giving the enemy one extra shot at you will add up to a lot of extra damage (and therefore a lot more scrap wasted on repairs) through the course of the game.
What most people don't know is that you can leave autofire turned on and not have your weapons fire if you don't want them to. You can even do "selective" autofire and have some weapons on autofire while others are not (which someone in this thread was wishing for).
Here's the trick (which I explained step-by-step in this missile defense thread):
Weapons will not fire unless you've designated a target. So for the weapons you want to fire continuously (such as Ion blasts), select a target location on the enemy ship, make sure autofire is turned on, and let it fire away. For all of your other weapons, do not select a target. If you accidentally select a target and you want a weapon to "hold fire" - simply select that weapon and then right-click on/near the enemy ship. That will clear any target you have designated with that weapon. This will allow you to hold off on firing weapons that you want to fire in a volley, while not stopping your other weapons from firing as fast as possible. When you're ready to fire multiple weapons in a volley, simply pause the game, target the enemy ship with each weapon, and unpause. If you want them to fire in a volley again, simply pause the game (after the weapons all fire), un-target each weapon, and unpause to let them all charge up again.
The nice thing about this technique is that if you get caught up repairing your ship or repelling boarders and forget to un-target the enemy ship after a volley, your weapons aren't all sitting there useless. Also, you're often trying to do a volley or two early in combat, to take down the enemy's shields or weapons. Once those are down, you want rapid firing of everything to deplete systems or the enemy's hull as fast as possible (especially if they're trying to repair a system and you want to keep it damaged). So leaving the weapons on autofire guarantees you'll hit the enemy as fast as possible (simply stop un-targeting the weapons after they fire, and leave autofire on).
I'll try to post a video in the next day or two, illustrating this technique. Its definitely easier to show than explain.
Enjoy,
--Noel