Matsue City Hotel
A quirky business hotel. Although fine for a solo traveler, avoid double occupancy as the rooms are small even by business hotel standards and the so-called doubles only have one single bed. The hotel is easy to find, with a large clock tower on top; in fact, the owners have sprinkled their collection of antique clocks and other furniture throughout the hotel. Take the bus from JR Matsue Station to Ohashi Kitazume about 6 minutes, last departure 9PM.
Terazuya Ryokan
Nothing fancy, just a pleasant family run ryokan with shared bathrooms and Internet access. The hosts will pick you up at the train station. There's a nice shrine across the street.
Toyoko Inn
Conveniently located near JR Matsue Station. From the north exit of the station, cross the street on the left side and walk for about 2 minutes. All rooms have a TV, and the beds are quite comfortable. Internet access is available in the lobby, and coin laundry is available as well.
Tokyu Inn
Of course they're in Matsue! They're everywhere. This one is also a couple minutes' walk from JR Matsue Station.
Matsue Universal Hotel Honkan
Matsue Ekimae Universal Hotel
Business Hotel Lake Inn