If you are very interested in plants you would rate this higher. It was a relatively short stop - as the area is not too large and easily walkable. The plants/trees were well marked and viewing and photographing them was relatively enjoyable.
Combined Rainforest gardens, Mendenhall Glacier and State Museum tour. The tour included two of the highest rated sites (glacier and museum), only took a few hours and was relatively inexpensive. You could do these 2 on your own with the shuttle to the glacier and a moderate walk to museum and save a few bucks. Mendenhall is impressive and there is a lovely waterfall (via a moderate walk) as well as a nice visitors center. The State Museum is also recommended as it gives a very good overview of the native cultures, gold mining history and information on wildlife, geography, etc. We also walked around town and visited the unimpressive Capitol Building (with a self guided tour) and the outside of the Governor's Mansion and, of course in town shopping.
There were no "must see" places according to the tour books I read. Saxman Village turned out to be a worthwhile visit with good introduction to the native people and the best selection of totem poles - not too expensive either. Difficult to do much in Ketchikan in 4 hours, so this tour provided some insight into native cultures and also gave us some time to walk around town. We did the Saxman village tour first to avoid any possible crowding in town when the ships unloaded. The flight to Misty Fjords is highly recommended but it was cloudy, rather pricey and my spouse is not a small plane person.
The railroad ride was very enjoyable. The scenery was quite nice and the commentary on the history of the railroad and area was another plus. It takes several hours for the trip and costs over $100, but it is one of the top attractions in Alaska. You can save a few bucks by going to the station in town and buying your ticket directly with the RR, but it may not be worth the effort.