There's a score bonus available on Stage 2: a small plane leaves its hangar and tries to take-off on the runway. If you destroy it on the runway, then you get a bonus of around 56k.
Other scoring tricks...I assume people already know about the Stage 4 boss-milking already. Stage 5 also has a few secrets (from Randorama's strategy guide on shmupsforum):
You need,when you arrive at the central platform that has two walker mechas on it,to make it arrive at the other side of the factory.This is done by leaving one of the two mechas functional, since the platform will stop moving if you destroy them both.Once it arrives at the other side, it will give you 3,279,650 points.Then, there's a section with round tanks moving on two planes: bomb them for 59,630 points each.This trick can be repeated four times, it is worth a maximum of 1,3x4=5,2M (more or less) in total.
Now, these tricks work on special version, while on normal version, the first stage 5 trick gives you only 300k, and the second one doesn't work. Also,on stage 4, since you have a less powerful bomb,you need to be careful on how to use it (place yourself at centre of the two ramps, at about half of their length).
