My wife and I did an Alaskan cruise for our honeymoon in 2006. We had a great time and would go back there in a heartbeat. We stopped in Juneau, Skagway, and Ketchikan. It was raining in Juneau, so our helicopter outing to a glacier was cancelled. We ended up going to the Red Dog Saloon and did shots for 2 hours (be sure to order a Duck Fart). We walked around the downtown area for a little bit and looked through the shops, but didn't do much else. When we got to Skagway, we realized that the shops were the same as the ones in Juneau. We were scheduled to do a rafting trip through a Bald Eagle preserve, but our ship was leaving early, so we had to cancel. After doing a tour of the Red Onion Saloon (nothing special), we ended up stopping in one of the offices in Skagway offering tours and did a 3-4 hour van tour that went out to the Yukon Territory in Canada. It's the same route as the train tour in Skagway. The scenery was beautiful and we saw 4 bears along the way. It only cost us $60-70, which was a bargain compared to the cost of some tours. In Ketchikan, we gave the shops about 20 minutes and then walked around until we found a place offering flight tours of Misty Fjords National Monument. Since our helicopter tour was cancelled, we decided to do take the flight. This was probably my favorite thing we did. The tour ran about an hour and a half. I was able to sit in the co-pilot's seat on the way out and had spectacular views of the fjords.
Definitely find things to do in each stop. The shops are the same everywhere. What made each stop for us were the excursions. We would go back there in a heartbeat. Like Goose said, you'll see scenery that you don't see anywhere else.
Gig 'Em,
Whoop99