The Shop Manager now supports a new shop option called "price formula". This allows you to set the price of a good using a formula.
The basic use case is to allow you to enter arbitrary prices (for example, an easy way to set prices over 999999).
The real power of price formulas comes in when you begin using formulas. For example, you can base the price on game variables or switches to have the prices fluctuate over-time. You can base the price on your actor's levels or stats. Perhaps you have a script that provides you with a "merchant" skill level, and you want to base the price on this skill level.
As with any other shop option, they apply to a single good for that specific shop.