Skagway
We booked a private tour with Becky McGill. Her company's name is Beyond Skagway.
http://www.beyondskagwaytours.com/index.html Becky allowed us to customize the tour to do exactly what we wanted. She was waiting for us at the end of the dock with her 7-passenger Suburban, and drove us up into the Yukon with plenty of picture stops along the way. We even came upon a bear eating dandelions at the side of the road.
She arranged for a private meeting in Carcross with a First Nations totem pole carver - DH is a woodworker and thoroughly enjoyed his time talking with Keith. We stopped at the dog sled camp and our DD's spent time with the puppies. We chose to have a picnic lunch, which Becky provided. On our way back to Skagway, we stopped and had our lunch at the edge of a lake. Along the way, Becky would borrow my camera and take candid photos of our family. She is very knowledgeable about the area history and is a delightful guide. I highly recommend her!
Back in Skagway, she took us to 2 shops that were locally owned and featured local artists with very nice merchandise. The owner of 1 spent a lot of time with us explaining the various artists and the mediums in which they worked. Unfortunately, the name of the shop escapes me.
Juneau
As PP said, the Wonder docks at the AJ dock. Disney provides free shuttle buses to take you into Juneau. When you disembark, you will see signs pointing you to the right for ship excursions and straight ahead for the shuttle buses. The buses drop you off at the Mt Roberts Tramway parking lot, which is at one end of the Juneau shopping district.
We ziplined with Alaska Zipline Adventures.
http://www.alaskazip.com/index.html This was my favorite excursion of the entire trip. The reason that I picked them over other zip companies is that their mininum age is 9 and minimum weight is 70 pounds. That way our DD10 was able to go. They provide rain jackets to put on over your clothes to protect them from dirt, etc, and all the zip gear. They spend a lot of time getting everyone geared up, including helmets, and checking everything before you zip. There are a total of 7 platforms with 5 separate zips. You have 2 guides, 1 to send you off and 1 to catch you. My favorite way to launch was to jump off the platform backwards and then let go of the tether line. Wahoo!!!
We had them take us back to Juneau so that we could spend some time shopping. Others in our group went to the glacier.
Ketchikan
We took a float plane trip to the Misty Fjords with Seawind Aviation.
http://www.seawindaviation.com/ This is a family business run by Steve and Leslie Kamm using a 7-passenger Beaver float plane. They are very nice people and Steve is a great pilot. The Fjords are gorgeous. Steve landed the plane on an alpine lake and we got out and walked around on a small island and took pictures. On the way back to Ketchikan, he flew us around several mountain peaks to show us the mountain goats. We also saw a bear. DH comes from a family of pilots, so on the way back to town, he sat in the co-pilots seat and he and Steve talked airplanes and flying. We were the last group of the day, so when we got back to Ketchikan, we were able to watch him drive the plane up onto the dock for the night. Leslie, her sister, and 3 DD's were there, so we spent some time talking with them. It was so nice to have that personal time, rather than being hustled back on a bus with 50 other people.
We did some shopping when we got back into town. There is a really big Christmas shop at the end of the dock right next to where the Wonder docks.