Taxis wait at the larger hotels and designated taxi stands in most of the larger towns along the peninsula. There are no meters; you pay a set fare based on the distance you are traveling. Ask around for the going rate to your destination and negotiate the fare with the driver before you hop in. Even the smaller towns often have a few taxis for hire near the town plaza or bus terminal.
Larger cities with their own bus systems (Tijuana [1], Rosarito [2], Ensenada [3], and Mexicali [4]) also have taxis de ruta (route taxis), which follow a set route, like a bus, but stop wherever someone flags them down or a passenger asks to get off. These taxi services use large American station wagons that hold up to 12 passengers. Fares tend to be marginally higher than comparable bus fare.
Links:
[1] http://www.moon.com/destinations/baja-cabo/tijuana-rosarito-and-tecate/tijuana
[2] http://www.moon.com/destinations/baja-cabo/tijuana-rosarito-and-tecate/rosarito
[3] http://www.moon.com/destinations/baja-cabo/ensenada-el-rosario/ensenada
[4] http://www.moon.com/destinations/baja-cabo/mexicali-san-felipe/mexicali