Anti-Missiles
This secondary weapon is a superb defensive system, most effective against enemy missiles. While it cannot totally eliminate the threat of these weapons, it can certainly reduce it.
The anti-missiles are fired automatically in response to incoming enemy missiles and other small objects. While the anti-missile projectiles are fast and home in on their targets, it is still possible for them to miss, or to hit another target instead. Therefore you cannot fully rely on them to shield you from all enemy missiles. Stay alert!
In addition to missile defense, the anti-missile weapon system provides a "last ditch" collision avoidance counter-measure: a red, short ranged anti-missile projectile that will target small enemy ships. Note that this system will only activate if it is detected that the (somewhat low) yield of this counter-measure would be sufficient to destroy the enemy threat and thus avoid the collision. Furthermore this weapon takes some time to reload, so it cannot defend against multiple simultaneous threats. Beware that this system is literally a final effort to avoid a collision with weak enemies: it should not be relied upon to make up for pilot error!
Missiles (Ammo)
This secondary powerup is fairly straightforward: it will gradually replenish your missile ammunition, up to the maximum number of missiles that your ship can hold.
If you like to use a lot of missiles, this powerup can provide you with a near-constant supply (unless you really like to use missiles - i.e. you're a missile spammer - in which case the rate of rearmament will not be sufficient to satisfy your gross misuse of this otherwise tactical weapon).
Secondary Shield
If you enjoy taking damage, or if you instinctively collide with enemy ships that you are unable to destroy by more conventional means, this secondary shield will keep you alive longer and allow you to continue these tactics! The shield works similarly to your primary shield, and provides an additional layer of protection.
When you pick it up a red bar will be overlaid on the shield indicator portion of the HUD, which represents the remaining power in your secondary shield. In addition to absorbing damage, this shield will gradually lose power over time until it eventually runs out.
One other feature that this shield provides in addition to the health benefits is the ability to protect your primary weapons from damage. While this shield is active, you will not lose any weapon levels, regardless of how much damage you take. This is a big deal if you tend to take hits fairly consistently and would otherwise lose weapon levels.