Stage Score - You get points for making contact and
generating blocks. For each chain step, you get points equal
to:
(# of blocks generated in chain) x 10 x (chain step #)
The first term includes all blocks generated by previous steps
in the chain as well as the current step.
Time Bonus - When you clear a stage, you get 100 points for every 3 seconds below 5 minutes you spent, up to a maximum of 5000 points.
Step Bonus - When you clear a stage, you get 100 points for every 3 steps below 300 you took, up to a maximum of 5000 points.
The biggest factor affecting your score is big chains. In addition to awarding large scores directly, they also generate lots of bonus blocks which help you clear the stage faster and in fewer steps for yet more bonus points.
Each chain step adds a number of bonus blocks equal to the
chain step number, or that number minus one, whichever is
even. For example, a 10-step chain gives you
0+2+2+4+4+6+6+8+8+10=50 bonus blocks.
There is a rule that the chain time limit (represented by "angel wings" when you make a contact) stops counting temporarily when the player character is falling. Thus if you're making a chain with a block which is falling a very long distance, you'll have to fall with the block or the chain will be broken.