Eating well is a bit of a problem in Dakhla, and I've found it's best to stick to the hotels. The food at the Desert Lodge in Qasr is an unexciting set menu of soup, meat, vegetables, and dessert, but the meal is substantial and the service is very pleasant. A few kilometers south, the Bir Gebel Hotel and Camp can supply a tastier, but rough-around-the-edges, meal of meat, rice, and a traditional dessert of agwa, a sticky, sweet mash of dates and olive oil that can serve as a meal in itself. In the central town of Mut, the Negoum and the Mebarez both serve passable food, and the restaurant at the Forsan is also decent. There are also several small local restaurants in the town. The cleanest are two on the main road into town from the north, close to the Mebarez hotel and across from the tourist information office, and they are explicitly aimed at the tourist market.
Note: This information was accurate when it was published, but can change without notice. Please be sure to confirm all rates and details directly with the companies in question before planning your trip.