First I'll tell you about what we did in the Alaskan ports, then I'll give you some websites to look at. If there are a few people traveling together, you might consider renting a car or minivan in some ports - it will definitely be cheaper than taxis or tour prices, but you'll miss the commentary and you'll have to navigate. These towns are so small that it's easy to find your way around. Be sure to reserve in advance because all the cars get taken when multiple ships are in port.
Skagway: The main sight is White Pass, the difficult route to the gold fields of the Yukon. There is a fully narrated narrow-gauge railway or you can opt for a bus/mini-bus trip up the highway like we did. Both let you see the river valley and take photos. The bus is cheaper and gives a view of the marvel that is the railway line. You could drive this yourself easily, just be prepared with your passports if you cross into Canada at the top, you'll need them on the way back. My in-laws shopped for the rest of the day, my mom opted for a longer tour into the Yukon, and the two of us took a catamaran across the straight and were taken by 4x4 bus to a lake where we canoed/motored close up to a glacier. It was enjoyable, but with all the other massive glaciers you see on this trip it was a bit underwhelming. Plus it was expensive because we couldn't find anywhere to book it except thru the cruiseline.
Juneau: A trip to Mendenhall glacier is cheap and worthwhile. If you don't rent a vehicle, take the blue bus (there's a kiosk in the parking lot with the others, it's only a few dollars each and goes fairly regularly, at most every half hour). You get funny stories on the way, and when you get there you can see the glacier across the lake, wander around the salmon streams (be the first ones there in the morning and you might see bears feeding on the fish), and check out the welcome center. We did a hike to the waterfall - maybe we took the wrong route but we couldn't see much of the waterfall even though we could hear it. The highlight for us in Juneau was a helicopter ride over 4 glaciers with a landing on 1 of them - expensive but extremely worth the money! We booked directly with ERA (http://www.flightseeingtours.com/content/index_eng.html) on the 4 glacier adventure. My in-laws did a bus tour in Juneau with a salmon bake or something, which they liked because they don't get around too easily.
Ketchikan: It rained and we didn't want to do another big tour so we did our own thing. Creek street is right near the wharf so we walked there and browsed the shops. There were no cars available for rent so we took taxis to Saxman Totem Village (close to town, but only good if you either really like totem poles or are with a tour that gets to see the native ceremonial dance show) and Totem Bight (far from town, ~15 min, but a more natural setting with interpretive panels. A tour group arrived while we were there so we attached ourselves to them to get the info.) My mom signed up for kayaking that ended up being canceled due to the miserable weather so she and I did more shopping, while the men watched a lumberjack show that was decent. If you want to get duty free alcohol, there is a little shop near the wharf that has good prices.
There are plenty of other options in each port - gondolas up to viewpoints, ziplines, glacier trekking, fishing, whale watching (I think spring is good for this), dog sledding, bear viewing, gold panning, horseback riding, photography, salmon bake and gold rush show... The shows, theme meals, and gold panning can be cheesy but a lot of people like that kind of thing.
We booked all but 1 tour independently from the cruiseline, and that one was only because it wasn't offered elsewhere. We booked everything in advance because of limited space, but there are always bus tours and such available when you get off the ship. Cruiseline tours are way overpriced but they have one advantage this is worth it to many people: if their tours have any problems it is their responsibility to get you back onboard the ship. With other tours there is a slight risk that you won't make it back to the ship in time, but the sole purpose of these Alaskan towns is tourism from cruise ships so they have every incentive to get you back to the ship on time. They are well aware of the ship schedules. If you have travel insurance that covers interruption then you should be covered if you miss the ship due to a tour being late, but this is very unlikely to happen and if it does you probably have bigger things to worry about. That being said, always travel with insurance! Travel agents sell RBC insurance, but I found TravelGuard was comparable in coverage and a fair bit cheaper, at least for travel over 31 days.
If you go to Sitka there's the Russian history and it's the best area to spot sea otters.
And now for some links:
All info about each port in Alaska
http://www.alaskaportreviews.com/
Go down the right-hand list to find videos of the cities you will be visiting
Large selection of Alaska shore excursions, including some triple-port packages for the 3 ports we visited.
http://www.shoretrips.com/common/search2.asp?rcode=PNW
Alaska excursions with extra info and thoughts
http://alaska.org/best-alaska-shore-excursions-alaska-cruise.htm
Popular tours, worldwide company - we booked the White Pass bus trip through them
http://www.portpromotions.com/alaska.html
Often recommended on cruise message boards. We booked horseback riding in Denali through them.
http://www.dollyvardenalaska.com/Shore%20Excursions.htm
Another big listing of tours
http://www.alaska-shore-excursions.com/
If you come across tours sold or operated by Gray Line beware. I have no experience with them in Canada, but in both Mexico and Australia they have had communication problems, operating problems, and false advertising.