Skagway - Railroad and then explore town on your own. We did Best of Skagway and didn't have any complaints about it (the Red Onion Saloon tour was really interesting and Liarsville was delicious and the performers really fun), but we regretted missing the town itself.
Juneau - Whale watching and/or helicopter glacier flightseeing. My parents loved whale watching. They also went to the Mendenhall Glacier Visitor Center but didn't want to make the long walk out to see the glacier a bit closer. My helicopter was truly spectacular. Mount Roberts Tram looked meh, with very long lines to board the gondola and it just goes up and gets a view of the Juneau area, which isn't as scenic as the other ports.
Ketchikan - someone else may have suggestions? A lot of people do lumberjack but that wasn't our thing. My parents did the rainforest and raptor sanctuary and really enjoyed walking around and seeing the birds and the guy carving totem poles. I did the Misty Fjords Wilderness Explorer, which is a high-speed boat that goes out to the Misty Fjords, which was gorgeous. The boat ride was fairly long (about 1-1.5 hrs each way), but it was beautiful scenery all the way along. There are a lot of seaplanes which go out to the Misty Fjords too. The town itself looks very cute, and again, I would have liked to see more of it. My parents did walk around a bit and liked it.