For tour stops:
In Ketchikan, we wandered around town one time and on the second, we did a flight seeing trip over Misty Fjords with
Family air tours.Excellent trip, excellent pilot, and worth the money.
In Juneau, our first trip we chartered a boat and went to Tracy Arm. We found a charter fishing guy who was willing to do a non-fishing tour (search juneau boat charter). It was expensive but we were the only people on the boat and the only people at the glacier, where we had lunch. Our second trip we went to Mendenhall Glacier and did a whale watching trip with
Harv and Marv. They fit 5 people on the boat, not the usual 50-200. It was an amazing trip.
In Skagway, our first trip we wandered around town. Our second trip we rented a car and drove up to Emerald Lake. The car rental was about $100 for the day and the trip was wonderful. We got to see some of the area, some bears, and Emerald Lake. Often, people take the railroad trip which I have heard is really good, but I hate crowds.
When we arrived in Whittier, we took a shuttle to Anchorage that went to portage glacier and the like. It took longer, but it was interesting. We rented an SUV in Anchorage and returned to the Kenai peninsula where we wandered around for a few days: Home, Seward, Cooper Landing. All are nice and worth spending time in.
Enjoy your trip! We loved Alaska so much on our previous trips we are now returning for the entire summer.