A great way to get points, though hard as it is, is to get the letters of CRISTAL in order. 150,000 bonus, not to mention wipes enemies out. Useful on a stage you've already screwed the big crystal order up on.

and it's orange counterpart are also useful point getters (50,000 if you get all the crystals, plus whatever crystals you got, however, note some stages are impossible to get them all)
Finally, the

,

and it's yellow version. They'll drop a bunch of crystals, based on the color of the fish (blue drops blue crystals, and so forth) once you beat all the enemies.
Oh, before I forget, the

will give you 2,500 points for every enemy still alive when you grab it. If you see it, try to avoid killing more enemies unless you have to.