Of course the budget is a key here. Flightseeing trips can be just spectacular, but they're really pricey.
Juneau - Get to Mendenhall glacier somehow. There are busses at the dock that will take you there. It's relatively inexpensive. There are some tours that combine Mendenhall with other adventures. At the end of the parking area is a bear viewing area, which is basically a wooden deck. We didn't see any bears on our visits however we did see many salmon spawning and that was intersting to see.
Whale watch trips to me are a must. You will most likely see whales from the ship but you won't be all that close. The whale trips to Auk bay are wonderful and you can get really close to see many whales. We used Orca with Capt. Larry and they were great.
Mt Roberts tram. Wait until you dock to confirm the weather's good. If it is then go up the tram. Wonderful views from up top. If you're afraid of heights I would think the tram ride would be pretty scary however.
Ketchikan - We love walking the down. Go up to Creek street, up the funicular and walk down the married man's trail. Very nice and cheep too.
We were there this time of the year and there were salmon flying up the ladder at creek street. You will see a lot of dead salmon. The funicular's cheap so it's a nice and inexpensive way to check out the town. The Duck tour was a lot of fun. Nice town tour and into the water as well. Goofy and fun. There are totems in town and behind the hotel at the top of the funicular however, even though we didn't do this, I hear the totem parks are nice as well.
Are you going to Skagway or Sitka? You don't mention either of those towns. Well, if you go to Skagway I suggest the White Pass rail trip. Beautiful and historical. A great few hours trip. We just walked around Sitka so have no real suggestions for you there.