We are taking a trip this summer
It'll be just me and DH (no kids to speak of yet), but hopefully I can still offer some suggestions based on what we have set so far.
In Skagway, we will be riding on the White Pass railway, which should be a relaxing excursion that all ages can enjoy. We will likely be booking an extended trip on our own through Chilkoot Charters (just Google the name for details on the various White Pass-type trips they offer) that will take most of the day and let us sightsee by both rail and bus, with lots of stops for sightseeing and wildlife watching. The White Pass has been repeatedly communicated to me as "THE must-do" in Skagway.
We will also be doing a floatplane to Misty Fjord - expensive, but supposedly worth every penny. We saved a good bit by also booking this on our own with the company Island Wings. Again, the scenery should be breathtaking.
We are a bit undecided on Juneau. I think we will be trying to offset the floatplane a bit by getting to Mendenhall Glacier on our own, exploring for a while, taking a ride on the tramway, and maybe (adult-only venture alert!) heading to the Alaskan Brewing Company for a tour and tasting (we are admitted beer nerds!). I would love to do whale-watching with Harv and Marv, but DH is less than enthused (boo!).
I will say that I was very hesitant at first, but upon contacting specific companies and doing research here on the boards I will also concur that you should *not* be afraid of booking excursions in Alaska on your own. The tourism industry completely supports most of the lovely little towns that you will visit, and the businesses there wouldn't survive if they didn't deliver on their promises to show you a good time and safely see you back to the boat. In particular, Island Wings brags that they have not had to pay for a single customer to meet their ship at the next port in 25 years of business. So...do you homework, because it should be well worth the effort.
Also - when are you sailing? Take a look here on the DIS, because inevitably there will be a thread begun as a meetup for your sailing. Talk to others that will be cruising with you, as they will both have good advice and will be organizing some fun activities on board.
Happy sailing! This is going to be a terrific trip for us both!