Points are awarded for vanishing tiles. The larger the number of vanishing tiles, the higher the score, in a nonlinear almost-exponential sort of way.
This score is also multiplied by a Level Multiplier.
At the end of the level, if you used less than 100 moves to finish, you get an extra 10 points for every move less than 100 that you used.
If you manage to make all of the tiles of a given color or pattern vanish in a single move (a so-called Color or Pattern Blast), you get awarded significant points. If you manage to do this for more than one color or pattern, you get even higher bonuses!
You get special points awarded when you cause a "cascade." A cascade is when one set of vanishing tiles causes another set to vanish in a chain reaction. The larger the number of cascades you cause, the higher the bonus!
There are also special cascades:
If, in either of these cases, you have no orphans, you will receive a Deep Magic charm or a Magic Shift charm.
As you progress in the game, you will probably accumulate orphans. Once per level, you may click on the orphans, and play them like a Poker hand. There are rewards for having a Flush, Four of a Kind, Full House, Three of a Kind, Two Pair, or a Pair. If you don't have a pair or better, you will be penalized, so play carefully!