The Juneau hostel is nice, and cheap ($12 cash last summer), and right downtown (on top of the hill). Downtown Juneau is very walk-able. Juneau/Douglas have a nice bus system, but it would be a lot easier/enjoyable to get to certain places by car. The Mendenhall Valley camp ground is pretty nice, close to a bus stop, has a good view of the glacier, and even has showers. Douglas is beautiful too and not too far from DT Juneau.

Ketchikan was my favorite place, and has incredible salmon fishing mid summer. There is a pretty good bus system too. I stayed at the hostel one night and it was enjoyable, (it's a bit of a hike up a hill to get to it) somewhat expensive, though. There are a couple of great camp grounds with trails around them. I stayed at Settlers Cove, which is right next to the water (I helped build a guardrail and some steps on the trail to the beach). I also stayed at Ward Cove (surrounded by some great day-hike trails). You will need a car to get to either of these, though. Ketchikan also has some great totem pole parks. Misty Fjords National Monument is worth mentioning - but you need a boat or pay for a tour to get there. I spent a month in Skagway, but most of my time was spent working on the Chilkoot Trail (3-5 day hike end to end). I went on an 1 hour guided raft tour on the Chilkat river (bring some drinks and relax) which was a lot of fun. There is no bus, but you can get most places by walking (unless you want to go to Dyea). The hostel is nice and right down town. There is a guided train ride to and from the Yukon (end of the Chilkoot Trail).

If your trying to save money, don't pay for a cabin on the ferry. I took the ferry at least 5 times last summer and they were never crowded. There was always plenty of room to spread out on the floor (or in a seat if you can sleep like that). The solarium is heated, you can sleep up there, and even pitch your tent if you want to. I never had problems sleeping. It's hard not to see whales if you look hard enough, but you might get lucky enough to see some up close.

One thing I noticed about the ferry terminals is a lot of the stops are not within walking distance to town. Also, bring your rain gear, because SE Alaska is WET!

Hope this helps.