Disney dollars can be used at most (but not all) of the restaurants at Walt Disney World. Some of the restaurants that are located at WDW, but not owned by Disney, may choose not to accept Disney dollars. I have never seen a specific list of places that do not take Disney dollars, but you can get a good sense of the situation by looking at the brochure for the Disney Dining Plan.
To download the brochure, click
HERE, then click on the Disney Dining Plan card, then click on "Download Disney Dining Plan PDF." If a restaurant does not participate in the Dining Plan, then it's a fair guess that they will also not accept Disney dollars. An example of this is the T-Rex Cafe at Downtown Disney, they accept neither Dining Plan credits nor Disney dollars.
But again, the VAST majority of restaurants and shops at WDW do accept Disney dollars as payment.