We've done the Alaska cruise three times. Here are our favorites:
Juneau.................................Whale Watching and/or Mendanhal Glacier
Ketchican.............................. Misty Fjords (Plane/Boat tour) The town is cute too though!
Sitka..................................... Explore the city on your own
Skagway.............................. Car Rental (lovely drive out the only Hwy)
Many people like the train ride. We hated it and felt like we were at Disneyland. But we live in an area very similar to the terrain of the train ride. Anyway for us it was a complete boring event and the "Goldrush Town" was even worse.
Victoria.................................. Either explore the main tourist waterfront or go to Butchart Gardens, limited time though. We usually find a highly rated restaurant and have a special dinner to celebrate the end of the cruise. By then you are sick of cruise ship food.