Lunch at Tracy's Crab Shack at Juneau is a must-do. The line will be out the door but it moves at a very reasonable pace.
We thought our cruise was perfect, and here's what we did:
Vancouver morning of cruise: Fly Over Canada (right next to the cruise port)
Skagway: Glassblowing at Jewell Gardens, followed by a tour of the Gold Rush cemetery and short walk up to Lower Reid's Falls. This was all on our own, walking through town.
Juneau: Took a local bus (paid on the spot, no reservation) to Mendenhall Glacier, walked around there on our own and returned when we felt like it. Lunch at Tracy's Crab Shack, followed by the Mount Roberts Tramway, which is right by the crab shack (and both of those are also by the bus loading/returning areas for trips to Mendenhall Glacier.
Ketchikan: Island Wings seaplane tour of the Misty Fjords. Very experienced & safe pilot who is the only pilot for her plane. Plane is vintage so expect it to be loud. She provides headphones.
Vancouver afternoon of debarkation:
DCL post-cruise bus tour that went to Stanley Park, drove through Chinatown, then gave us about two hours to explore Capilano Suspension Bridge park on our own. Dropped us off at the airport. This was the only excursion we booked via DCL, and we booked it onboard. Afterwards, on our own we took a cab to and from VanDusen Botanical Gardens, which is a huge and varied set of gardens and includes a very nice hedge maze.