Powerups function in a variety of ways, but basically it’s a method of giving the player something in a way that requires them to make use of the two main mechanics of the FPS- Moving and Shooting.
Any powerup that replenishes something the player has in limited capacity has a variable value. The player only wants health pickups when he does not have max health, and his motivation to look for health pickups is proportional to how low his health is perceived to be.
Required pickups have high value, as they are required to progress in the game. Keys, for example, are required to get through doors in the level, or possibly activate machinery or bypass other “hard checks”
powerups that have a very high, or infinite capacity have a more stable value- pickups that add points, for instance, or currency. The player’s motivation to collect these is more dependent on player goals, rather than player needs. If the player wants to buy a shiny new gun, he will be more motivated to seek out currency pickups.
Powerups that add to or change game mechanics on a temporary or permanent basis are also very valuable- and when and where they are dropped takes additional consideration based on the behavior you want to encourage in the player. Invulnerability removes the self-preservation aspect of play, and allows the player to “cut loose” for a limited time. This power is best utilized when there is something to “cut loose” on, that grants the feeling of power. Dropping an invincibility powerup in the middle of a gang of enemies creates both a challenge and reward at the same moment- the challenge of getting to the pickup, and then the reward of destroying the enemies in a fury.
Deferred-use powerups- (ie. Ammo) can be given to the player at any time, to be used later. This allows some room for less linear levels, as the player can explore and not necessarily need you to feed him health/ammo pickups constantly. However it is worth keeping a rough estimate of what supplies the player could likely have at a particular point in a level, so that you can design areas that make the player more desperate to find a particular resource. For instance, if you place a lot of “bullet sponge” enemies in a level with few ammo pickups, you raise the value of each bullet. Placing an ammo cache deep in the level is then like finding an oasis in the desert and is very empowering to the player.
Recently, DOOM has been lauded for it’s “glory kill” mechanic that grants the player health for close-quarters takedowns. This drives the player towards the enemy when he is low on health- creating a more frenzied, exciting experience when health is low.
[EDIT] Apologies, just now saw that your genre wasn’t FPS, but most principles still actually apply- powerups give the player a reason to shoot at something and move to a position. You can use powerups to create risk/reward scenarios where the player must complete a more risky maneuver to be rewarded with the powerup. Keep in mind that powerups that allow you to do something are more exciting that powerups that increase the high score.