Hotel J. B. Martinez (tel. 504/754-7154, US$9 s, US$12 d) is a new hotel in San Juan [1], with 12 pretty nice rooms around a small courtyard, all with private bath.
There is a simple but attractive cabin in the hills available for tourists, run by Jesús Castillo, for a mere US$3.70 per person. Reservations can be made through Gladys at the tourist office [2], or if you speak Spanish, you can call Jesús directly at 504/9658-9629. Jesús will also prepare meals (US$2) and arrange trips, horseback riding, etcetera, at a charge. Tips are welcome.
There are several comedores sprinkled throughout town.
Links:
[1] http://www.moon.com/destinations/honduras/western-honduras/gracias-and-the-lenca-highlands/san-juan
[2] http://www.moon.com/destinations/honduras/western-honduras/gracias-and-the-lenca-highlands/san-juan/sights-and-tours