We recently did the drive from Skagway to Whithorse and return. It was one of the highlights of our Alaska trip. Agree with OP comment about Emerald Lake - it is spectacular.

We're not railroad buffs so we opted to rent a car (Avis and a local company are available). We made a zillion photo stops along the way and stopped along the way to enjoy nature and picnic.

We shared Carcross with a tour bus, so the General Store and Museum/Ticket office were packed. Whitehorse is an interesting town to walk around, stop at the Visitors Center and visit the museum nearby.

But the highlight is the natural bueaty of the route. As an added bonus we saw bears along the side of the road - not to far out of Skagway!

In Juneau, if you have a car a drive north of town (I think the road ends 40 miles out) is a very enjoyable way to spend an afternoon.

Also In Juneau, if you like crabs - stop at Tracy's Crab Shack (it is really a shack) - for Alaskan King Crab clusters and great chowder.

Hope this helps.