We've done what you are doing twice, and also just cruised once - would agree that the WhitePass Railroad is great in Skagway, or if you are tired of trains after your land tour (we'd had enough the two times we'd were on the land tour), then rent a car from Avis and drive up to Carlock. You'll get to see the same scenery as the railroad, but you can stop whenever you want. At Carlock, you can also see sled dogs. If you don't go do either of those, Would also recommend the dog sled tour in Skagway.
In Juneau, you can't go wrong with Harv & Marv's whale watching, or the Princess excursion to the glacier combined with the whale watching tour. Or you could rent a car there from Rent A Wreck, and drive up to the glacier, then go to the Alaska Brewing Company for their free tour (one of our personal favorites), then drive out to the Grotto of St. Therese and see some beautiful scenery and many, many whales. In fact, you see the same whales you'd see on any of the whale watching tours, except you don't have to take the boat out.
In Ketchikan, there is the Deadliest Catch boat tour, the lumberjack show, and Dolly's House. Any tour of the totem poles is also great.
If money is no object, the flight to the glacier, dog sledding on a glacier or a bear watch are supposed to be the top of the line - I don't know personally, since these are always out of my price range.
Don't know if any of this helps, but would be happy to answer any questions if I can.
12Cats
