KAMUI - ALL Clear 35.5 Million
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KAMUI, released in 1999 by Siter Skain, even now still holds its place as one of the best doujin shmups ever made.
Siter Skain eventually went on to make the Tale of ALLTYNEX trilogy but I still think that Kamui is the best of the three if only because of its simple but elegant scoring system.
As you might be able to tell the game draws a lot of inspiration from Rayforce in both the mechanics as well as bosses/backgrounds and thus all the enemies are either in the foreground or in the background. In the foreground you can shoot them with your shot and the powerful laser which also cancels bullets. Enemies in the background you can lock with screen-wide homing lightning.
For scoring you want to kill as many enemies as possible in the background since you get a multiplier for doing that unlike killing them normally. How high this multiplier is depends on how charged up your lightning meter is when you release the locks with a maximum of x16 when the meter is fully charged. You can accelerate the rate of recharge by holding the lock button.
Another important trick in this game is something I like to call "deathlocking". Some enemies when they are killed drop to the background for a few frames before they explode and in that short instant you can lock them with homing lasers.
Nyu Media localized the game and can be gotten through Steam among others:
http://store.steampowered.com/app/283820/?