I stayed at the Apollo hotel. It's right in the centre. A good hotel with a friendly staff and a good breakfast too. The rooms are large and each have their own bathroom / toilet. The only problem in this hotel that it has no airconditioning, so it can be hot in summer :-( They should do something about that.
We've stayed here before I moved to Nijmegen itsself. It's quite a decent hotel right in the middle of the city center but very cheap. For the price you pay, you get a nice size room and breakfast!!
Directions: Right above the Kijkshop, almost next to the ABN AMRO bank in the city center. The picture shows you the view over the most crazy roundabout in the Netherlands, the Keizer KarelPlein