Advanced Cluster Missiles
Found in: Prisoners of the Maw
In between the weapons storage and communications tower, there's a dome. Bomb it for the upgrade.
Advanced Concussion Missiles
Found in: Imperial Academy Heist
In your Y-Wing, fly through one of the hangers at the academy.
Advanced Lasers
Found in: Battle of Hoth
After the AT-ATs blow up the shield generator, fly back to it to find the upgrade in the rubble. These are VERY helpful.
Advanced Proton Bombs
Found in: Razor Rendezvous
Go as fast as possible to the other side of the Star Destroyer to see a Llamda shuttle. Kill it for the upgrade. It will run away if you wait too long.
Advanced Proton Torpedoes
Found in: Ison Corridor Ambush
At the beginning of the level, dive down under the Frigate to fly through a large piece of debris. The powerup is inside of it.
Advanced Shields
Found in: Death Star Attack
At the start of the 2nd stage, dive close to the ground. Turn about 15 degrees to the left. It's sitting on a small building next to a turret.
Advanced Targeting Computer
Found in: Strike at the Core
At the final straightway before the core, fly under some pipes on the right side.
Cluster Proton Bombs
Found in: Imperial Academy Heist
Take a speeder during the night and fly through the hanger on the opposite side of the academy from the Concussion Missile Upgrade.
Homing Cluster Missiles
Found in: Battle of Endor
The power-up in this level stays in the same place the whole time, and can be acquired at any time - the difficulty is that this is a very large, open, and distracting map. Although it is sitting at a fixed point in space, the planet below you combined with the battle above you and the background with additional ships, stars, and other images simply make it hard to find.
To find it at the beginning you can choose to fly straight from the starting position (don't move) and try and look for a glimmering spot diagonally downwards and to the left of the leftmost Star Destroyer (the power-up is at about the same distance from you as the Star Destroyer).
The easiest way, however, is to destroy the left Star Destroyer. Wait until it falls all the way and stops. While it's hanging there in space, fly down underneath it and find the white area that you could potentially fly into (the hangar). The upgrade will be inside the ship where you can't see it, but if you fly into the hangar you'll be within the distance needed to grab the power-up anyways - make sure you have sound on so you can confirm you received it.
Homing Concussion Missiles
Found in: Raid on Bespin
Take out the balloon at the beginning, and head to the second platform. Blow up the tanker, and in the rubble of the tanks will be the upgrade.
Homing Proton Torpedoes
Found in: Vengeance on Kothlis
Once you get to the Destroyer, fly through a hole on the left side of the bridge.