Seymours on Lydiard is my current favourite. Beautifully appointed rooms with free wireless broadband. All depends on how long you want to stay though. It isnt right in the centre of town but just up the road from the railway station - about 5 - 10 minute walk into the centre of town. It's a refurbished older building and has a nice restaurant downstairs.
We had a nice two bedroomed house just off the lake through
Stayz - No 1 in Holiday Accommodation Rentals when we stayed for a week.
There are also some nice serviced apartments pretty much opposite Sovereign Hill but I prefer being closer to the centre of town (and the MIL).
Going in June, take your fur lined knickers, it can be deadly cold down there!