In Skagway the famous White Pass Railway is a thought. They also do a bus tour that is parallel to the railroad tour. That one makes stops if you want to take photos. It's prretty spectacular. We did the helicopter to the glacier in Skagway since there were other things we wanted to do in Juneau. It was wondereful and you can do them both while in Skagway.
My all time favorite tour in Ketchikan is the flightseeing to Misty Fjords. Misty Fjords is a National Park. It's an already glaciated area. Totally wild with waterfalls crashing down from high cliffs into the fjords below. You land on a mountain lake and the only sign of civilization and humanity is the plane and its occupants. The silence is deafening. It's totally awesome.
Last year in Juneau we did a half day fishing trip on a boat that my family chartered(4 of us)and had the time of our life. We saw wales everywhere and caught our limit of prize King salmon. The fight realing in these fish was incredible. My two teenage son's said they would never forget that day and our fishing trip.(it was expensive about 150 a person but worth every penny). We booked this trip on our own using Orca Enterprises which is off the pier on the main street there when you ship docks.
We will be back to Alaska in 2003 on the Summit or Coral Princess....its my favorite cruise destination( we have sailed there 4 previous times) Once on the Infinity,Mercury, Legend of the Sea's and Regal Princess. (we much prefered the Mercury to the Infinity)
Enjoy your cruise the scenery is unreal.
In Skagway, we did the White Pass & Yukon rail trip and enjoyed the experience and the scenery.
In Juneau we booked a half-day whale watching trip with Orca Enterprises in the morning. Our shuttle driver dropped us off near Mendenhall Glacier and we walked over there to see this magnificient glacier and then took the blue-bird bus back into town. We skipped the tram since the skies were overcast and the clouds were low enough to preclude us from seeing much from the top.
In Ketchikan, we walked up to the Totem Heritage Center and the salmon hatchery. Walked back into town via Married Man's Trail. That afternoon we had a spectacular excursion to Misty Fjords -- went out by catamaran and saw seals and orcas, and returned by floatplane.
Out of Juneau on a trip we did the white water rafting starting at the Mendenhall Glacier. About 10 people in a boat with a guide. Enjoyable.
I have not done the Skagway rail trip, but have heard wonderful recommendations on it.