My take (and, by the way, I wrote the Fodor's guide Suzy Q mentioned, along with a half dozen other guides to Belize):
All the properties mentioned in this string are good spots, though they each have pros and cons.
For value, cleanliness and overall appeal in the budget range in and near San Ignacio, you can't beat Aguada (across from Loma Luz hospital, a short taxi or bus ride from San Ignacio town), Martha's and Casa Blanca Guesthouse. Nefry's, a new place, I hear good things about but haven't stayed there myself. Also, Cahal Pech village is staging a comeback. For value outside San Ignacio, The Trek Stop is great. Ditto several places on the Mopan River, like Clarissa Falls, Cohune Palms and Parrot's Nest (though the shootings and such at Bullet Tree Falls are starting to bother me).
For value in the a-step-up lodge category, I like Crystal Paradise, Black Rock and the safari camp at Chaa Creek. Back near Belmopan in this mid-range, I'd choose Pook's Hill and Banana Bank.
I definitely agree that if staying outside town and properties along the highway like Trek Stop it's good to have a car. Otherwise you'll spend a fortune on taxis or a lot of time bumming rides.
--Lan Sluder
www.belizefirst.com