We used Expedia pretty exclusively for research and booking, and also stayed at two Comfort Inn properties. So, don't overlook your favorite chains while traveling - they often offer good accommodations at reasonable prices.
TOKYO: We stayed here at both ends of the trip, at Comfort Hotels. Either they do not have family rooms, or they were already booked - we needed 2 rooms for 3 people. Comfort Hotel Tokyo Kiyosumi Shirakawa was located right next to the Kiyosumi subway station, so that was great. Rooms were extremely tiny though, for two people. Location was a little out-of-they way, and dinner options were very limited. Comfort Hotel Tokyo Kanda Hiragashi had larger rooms, and a better location about 1/2 mile from Kanda Station. At both locations beds were comfy, pillows were awful (but you could get extras, so that helped). Sizable breakfast buffet was included and featured Japanese and western options. Average per night cost per room was about $93.
HAKONE: We stayed at a ryokan, a Japanese hotel that usually features Japanese style sleeping rooms and onsen, the hot baths. Although not always more expensive, ryokans tend to cost a more and you can add all kinds of extras like traditional Japanese dinners, etc. We stayed at Mount View Hakone (you can read more about it in the Hakone post), and added breakfast both mornings and dinner both nights. It was excellent, but not sure I would do two of each again, just from the variety and price-point perspective. This was an Expedia booking, held with my credit card but cash upon checkout. $360/night including meals, for 3 people.
HIROSHIMA: We stayed at the Hotel Century 21, in a room that had not been updated since the late 20th century. Location was excellent, just across the river from the train station with lots of access to the bus loop and restaurants. Hotel was very nice, but our room was an odd combination called a Japanese Western Style room that featured a small Japanese sleeping room and a very tiny sitting area. The futons were simply another quilt on the tatami mats, and I pulled out a couple ratty-looking futons from the closet to add a little more cushion. Luckily we were only there one night. Another Expedia find (this one charged to my card via Expedia), $135/night for 3 people.
KYOTO: You can check out an entire post on this hotel, but this is a classic example of how spending just a bit more than your usual can pay off big. Average price at the Kyoto Brighton Hotel was $250/night for 4 people and did not include breakfast but the other amenities made our Kyoto stay so much more efficient and comfortable. Huge room and bathroom, quiet residential location. Free shuttle to the subway, taxi stand right at the hotel, concierge desk with good English speakers, all kinds of maps including walking tours and area restaurants. Another Expedia find.
KANAZAWA: We tried to find a ryokan here but nothing really came up in our price range, so we ended up at the MYSTAYS Kanazawa Castle, which is not really anywhere near the castle. MYSTAYS is a Japanese hotel chain, and this hotel was in a great location just a few blocks from the train station and all the bus loops, plus lots of food options. Room was a little cramped with 3 beds and luggage but hey, it was $103/night for 3 people.