I personally love walking and biking tours. In Skagway, we did a bike ride out to a glacial plain that was wonderful. (I had pictures posted, but freaking Photobucket screwed me.) I really enjoyed that a lot. If you don't want to be that active, there was also a small bus tour in Skagway, hosted by a 19th-century woman (in character, obviously). That was also kind of fun.
Our wildlife preserve tour in Ketchikan was very wet, as it rained on us the whole time. We did see some interesting animals in captivity at the end of the tour, but we didn't see much during the tour, except a bald eagle did swoop down over us.
In Juneau, we did a whale watch. It was, unfortunately, very disappointing. But it's always very random on a whale watch. Sometimes the whales swim up to your boat (like our first Alaska cruise in 1988) and sometimes you don't see a single whale. Ya pays yer money, and ya takes yer chances.