You can take the same percentage off from the REGULAR price.
So if, say, Mario Kart: DD was on sale for $39.99, you'd still take the percentage off from $50.
However, if it became player's choice or something and a universal price drop to $30 occurred, then you could take the percentage off the $30 (since that would be the new "regular" price).
Basically, you just wouldn't use the raincheck on a SALE price.