Juneau - Definitely Mendenhall Glacier and whale watching (a combined tour we booked through the cruise line). If you book on your own, and the excursion is late, the ship may leave you and its then your responsibility to get back to your ship at the next port. Also be sure to check out the Red Dog Saloon, you will love it.
Sitka - We did a hike through the rain forest (also booked through the ship). We also did a boat trip to a salmon hatchery.
Ketchikan - We did a trolley tour around town but you can also do a walking tour on your own with a guided map. Check out Creek Street (the old red light district) or the lumberjack show.
Have a great time, you will be ready to go back again. We have done 2 different cruises through HAL to Alaska (different itineraries). Want to go again.