Ketchikan - I did the Misty Fjords Cruise / Flight. Didn't like it much. All you saw were islands with trees and trees and more trees. The flight was interesting, but I didn't think it was worth the 2 hours of boredom on the boat. You'd be better off doing a Totem Pole Tour. I wish I would have done that instead.
Juneau - We did the Evening Whale Watch and LOVED every minute of it. Saw lots of whales, bald eagles, seals, and even a bear.
Skagway - The White Pass Railway is a must do. My father did the all day one where you take a bus into Canada and then the Railroad back. I just did the Morning one and still had time in the afternoon to go horse back riding. Either one is great.
Victoria - I wouldn't know what's good or not. Our boat crashed against the pier, so we didn't have a chance to get off the ship...hehe.
Enjoy your cruise! I hope everything goes smoothly for you.