There's a huge variety to excursions to choose from so it really depends on your interests. We were on the Sun Princess last May and I was very happy with the two we took:
In Juneau the 'Helicopter Glacier Discovery' - expensive, but worth every penny. The weather was bad most of that day and almost all flights were cancelled; but we were lucky, and on one of only two flights to go out of about twenty. There were only four passengers (normally six) and we got about ten min. extra 'air time' and spent twice as long on the glacier as normal.
In Skagway we took the 'Yukon Territory Adventure' bus tour. It leaves first thing in the morning and is rather long (about 7 hrs.) but has lots of stops. For about the same price as just going to the White Pass summit on the train, you continue on through Tormented Valley, the northwest tip of B.C. and to Frontier Heritage Village just beyond Carcross in the Yukon for a BBQed chicken lunch. We stopped at Carcross for about 1/2 hr. on the way back, and it had turned into a beautiful day for the ride back down to Skagway - spectacular! We asked to be dropped off 'downtown' and still had plenty of time to walk around Skagway when we got back.
In Ketchikan we did no tours, but I have read the Misty Fjords seaplane flightseeing is fantastic.