The NH Zurbano on the Calle Zurbano, 79-81 (metro: Gregorio Maranon) is quite nice, and very conveniently located for the minsteries and government research centres (CSIC). It's abut 1 km from metro Nuevos Ministerios, which is on a direct line to Barajas airport. About 2 km from Puerta del SolGood deals are available online if you book ahead (65-80 euro per night, room only) and prepay. It's very clean, quiet and friendly.
Don't bother paying for breakfast, there are plenty of cafes nearby for a coffee and pastry.