Steff, first of all check out www.AlaskaPortReviews.com
for a ton of reviews and information about each port you are visiting.
The satisfaction rate of Alaska shore excursions is excellent and you can't go wrong no matter what you do. It just depends on what your personal tastes are. If money is no object, here is what I would choose to do.
Juneau: Helicopter tour of Mendenhall Glacier with a glacier landing and then shopping, followed by drinking at the Red Dog Saloon.
Ketchikan: Misty Fjords Float Plane trip with a landing, followed by shopping and maybe salmon fishing off the Creek Street Bridge (September is prim salmon fishing time) It is catch and release and you can rent a rod and a buy a one day fishing license right by the creek.
Skagway, I would do the White Pass Railroad tour followed by a hike to
wer Dewey lake, followed by a shopping tour of Skagway and drinking at one of the local bars.
Shopping will be fantastic for all items, as the shops are discounting by at least 50% to turn their inventory over before the end of the season (mid-September)
Hope that helps.