We just went on the Golden to Alaska this past May and it was fantastic!!!
Skagway: Another vote for the White Pass train. We did a tour that also had a driving part up into the Yukon where we got to see some bears. Awesome.
Juneau: Definitely the best port to go whale watching. They were jumping out the water like crazy. Also, take the time to go to Mendenhall Glacier. There are lots of tours that do both.
Ketchican: Great town to walk around and do some shopping. I thought they had the best prices on lots of typical stuff. We also went flightseeing in Misty Fjord.
Victoria: Nice to walk around town. Also Butchard Gardens are beautiful at night.
On the ship, don't miss the talks given by the Naturalist that will be onboard. He was absolutely entertaining and wonderful. He had 4 talks spaced out over the week and each one was unique and added to the sights we were seeing on the trip.
While cruising through Glacier Bay, have your binoculars ready and listen to the announcements made by the Park Ranger. They'll point out whales, bears, and other neat things to look at.