During the ride you'll go through a dark tunnel with a laser effect. Spin around so your vehicle is facing backwards. Look to the upper right of the tunnel entrance you just went through and you should see two very not-noticable unmarked white-ish dots on the wall. Fire at them as much as you can!
In the very first room on the left, where the robot is. His hands are moving up and down, on the insides of his hands are two targets and one of them is a secret hot spot which boosts your points enormously!
The volcano in the neon colored room against the wall in the back is worth about 100,000! just shoot the targets that are not in plain sight.
As you leave the first shooting area, there is a "Z" target on the ceiling above you, if you hit the target directly in the center with the laser, you get 100,000 points per hit
there is a target in the first room worth 100,000 points. When you enter the first target room there will be an orange robot on your left. As you pass,spin around and shoot at the target on it's left arm. Each hit is worth 100,000 points.
There is also a hidden target on the wall in the room that shows you the wall video of the flying Zurg ship. You can only see it for a split second while the Zurg ship is stopped and just before it gets destroyed. This is the most challenging one to find and hitting the targe (Not Enclosed in a "Z") also gives high bonus points, but I don't know how much since you really have to concentrate on the wall.
In the 4th room: (first Zurg room) Bottom of Zurgs ship - 100,000