Juneau is lacking in nice hotels. Parts of the Baranof look like it hasn't been cleaned since the Hammond administration.

When I'm in Juneau, I always just stay out by the airport and use a rental car to get into downtown. With the big parking garage in downtown parking is never a huge issue.

There's a couple of decent Best Western's, as well as the Extended Stay, all by the airport. If you're dead-set on staying in downtown, I'd either go the B&B route or just settle for paying a lot of money for a rather mediocre room at a place like the Baranof.