Housed in one of Santa Rosalía [1]’s mining-era wooden buildings, the Hotel Blanco y Negro (Sarabia at Calle 3, tel. 615/152-0080, US$18–30) has been a favorite among budget travelers for many years for basic, clean rooms with private baths.
Terco’s Pollito (Obregón at Calle Playa, opposite Parque Morelos, tel. 615/152-0075, US$35) has seven rooms, with air-conditioning and cable TV; its reception area is inside the adjoining restaurant (7 A.M.–7 P.M. daily).
Two-hundred meters from the ferry terminal on Highway 1, Hotel El Industrial (tel. 615/152-1857, US$40) has safe parking, rooms with air-conditioning and cable TV, and 24-hour reception.
Hotel del Real (Montoya 7, no tel.), is another good option for an overnight stop near the ferry terminal. New rooms on the back side of the building have air-conditioning and TV for US$35.
The business-oriented 
El Morro Hotel (tel./fax 615/152-0414, hotelmorro [at] aol [dot] com, US$50) overlooks the Sea of Cortez about 1.5 kilometers south of town on Mexico 1 (btw Km. 194/195). Its 39 spacious rooms feature ocean views and remote-control air-conditioning, and there’s secure parking, a restaurant/bar, and swimming pool. Wireless Internet, included in the price, is available in the lobby area. This place is pet friendly.
At the edge of a cliff that drops into the sea, Las Casitas de Santa Rosalía (tel. 615/152-3023, mariahsantarosalia [at] hotmail [dot] com, US$60–70) has several modern cottages, plus a well-equipped gym, wireless Internet, and a terrace that overlooks the harbor.
In a French colonial building, the Hotel Frances (Don Gaspar 210, tel./fax 615/152-2052, US$75) overlooks the old copper-smelting facility on Mesa Norte. Its 17 rooms have high ceilings, cable TV, wireless Internet, and air-conditioning. There is a small pool in the courtyard and the hotel restaurant is open daily for breakfast only. Coffee only on Sundays.
Links:
[1] http://www.moon.com/destinations/baja-cabo/guerrero-negro-bahia-concepcion/santa-rosalia