My favorite place to stay in Juneau is Grandma's Featherbed Inn. It's owned/operated by Best Western. In the winter the rates are pretty competitive, about $85 or so. A full breakfast is included with made-to-order omellettes and an excellent choice of fruit and juices.
Each room is unique with antique furniture, featherbeds (on top of the bed), kitchenettes I think, and a JACUZZI!
I like getting a different room everytime I stay. They even have high speed internet in most rooms (if not all) and a terminal to use in the hallway. I think there are 14 rooms or something.
The only minus is that it's near the airport so far from downtown. If you have a car it isn't a problem. Best Western also has a shuttle bus that is pretty good about taking you wherever you want to go.
I've stayed at the Pioneer--large rooms but pretty old, nothing fancy; sort of downtown. And the Westmark--Fancy but small rooms and not worth the price in my opinion; downtown. And the Aspen hotel which has a very small pool--business style but I was not satisfied with the cleanliness (I'm kind of picky when it comes to bathrooms); right across airport parking lot.
The Fiddlehead restaurant (right by Pioneer hotel) has an EXCELLENT smoked salmon ceasar salad and good desserts.