That would depend on your likes and dislikes. There are many options and many price ranges. It also depends on what time period you are going to Alaska because Alaska has different things to see depending on the time of the cruise.
Some suggestions are if you can afford it a flight tour that lands on a glacier is really great but expensive.
If you want to see whales I would do this out of Juneau. The Mendenhall glacier is beautiful and if you want more activity a raft ride down the river is fun and not to hard to do.
The rainforest and totem parks are good in Ketchikan or if you feel a little more active take a kayaking trip out of Ketchikan. The lumberjack show in Ketchikan is a fun short tour.
In Skagway for me the views you get from the WhitePass Railway are fantastic. If you add a trip into the Yukon you will have a good day with a lot of beauty. You can also take a trip to Haines from here to see wildlife and may see whales on the way. You would get to see many eagles in Haines.
If you like fishing that can be done in any port. If you are looking to see salmon the end of June to the mid of July will be the heaviest salmon runs but also the wettest time of year.
If you just want to walk around the towns you can see some interesting things. If you are looking for shopping and want true Alaskan products your best bet is to not go on the main drags but to the shops further in town or on the edge of town. Look for the Alaskan markings to see if it is true Alaskan. Most shops on the main drags just sell the foreign stuff you can buy almost anywhere.