Uwajima Youth Hostel
Inconveniently located on Atago Hill to the south of town, a fair hike about 2k from the train station or an 8 minute taxi ride. Note also that they're closed on Sundays. They do offer bike rentals and Internet access, though.
Hotel Clement Uwajima
Business hotel connected to JR Uwajima Station, with a summer beer garden 6-9PM, ¥3600 all you can eat/drink.
Hotel Shirakabe
Cheap accommodations suitable for a quick trip; free washing machine and Internet are included.
Sunokawa Park Camping
A very pleasant seaside camping ground, located an hour down the road south from Uwajima on the way to Sukumo and Cape Ashizuri. Facilities include showers, toilets, barbecue pits and acres of grass.
Uwajima Kokusai Hotel
Luxury option in the center of town, with a large public bath, bar, cafe, and upscale restaurant. It's popular with tour groups, particularly folks in town for the bull sumo, and the staff will be happy to help with tickets.