The Beachside Villa Inn is a great place to start and end an excursion in Alaska. It is far enough away form Juneau that you aren't in the middle of the city, but it is right across the bridge. We like this place because it is so private and quiet, not to mention GREAT views! Plus there are large soaking and jetted tubs in most of the rooms, I think, and it is a great way to relax after you have been fishing or climbing or touring all day in the cold Alaska air.
The Beachside villa also provides snacks and breakfast, drinks and hot cocoa etc., which is nice since the average hotel wants to charge you $5 for a bag of chips, if there's anything at all.
The innkeepers will make sure you have everything you need without stepping on you toes, the way some B&Bs can be. Our room was spacious and had a private deck that allowed us to have wine in the evening and watch all kinds of wildlife and birds.
At $179, I thought the room was an amazing deal - a huge 2-person whirlpool, what hotel can you get that for less than $200?