A few ideas for on your own stuff that won't break the bank...(from the local) Juneau; Mendenhall Glacier. You can grab a cab (about 10 miles from town) or catch one of the tour companies up that way.
http://www.juneautours.com/juneau-city-and-glacier-tours/ Alaska Brewery. Again grab a cab or take the shuttle:
http://www.alaskanbeer.com/our-brewery/visit-the-brewery.html http://alaska-shoreexcursions.com/juneau Alaska State Museum: Alaska History and artifacts etc. Short walk from the pier, right in downtown Juneau. Right up the street is the Governor's Mansion (up a little hill) where Sarah Palin use to live. Yes you can see Russia from Alaska, no not from Juneau.
http://museums.alaska.gov/ http://en.wikipedia.org/wiki/Alaska_Governor's_Mansion Sitka; Sitka National Historic Park, 10-15 minute walk from the in town pier. Has a nice totem trail (about a mile long give or take) and visitors center with craftsman doing native Tlingit art. They also run the Bishop's House in town. (I think we're gonna tender here as the "dock" is pretty small for our size ship)
http://www.nps.gov/sitk/index.htm http://en.wikipedia.org/wiki/Sitka_National_Historical_Park St. Michaels Cathedral: Right in town is this small old church. The original burnt down in the 60's but the new one is nice and has lots of icons for those into that sort of thing. I think its a suggested donation of $5.
http://en.wikipedia.org/wiki/St._Michael's_Cathedral_(Sitka,_Alaska) Fortress of the Bear: About $50-60 roundtrip via a cab. They turned an old water plant into a bear rescue facility. If you want to see some brown bears up close, but not in the wild, this is your place.
http://www.fortressofthebear.org/ Alaska Raptor Center: About a 20-25 minute walk from downtown is this center where they rehabilitate eagles etc. It would be a 5 minute cab ride.
http://www.alaskaraptor.org/SITE/index.html Sheldon Jackson Museum: This museum of native artifacts and life is on the way to the national historic park. About 5-10 min walk from town. Definintely worth a visit in conjunction with the historic park. Sheldon Jackson was a presbyterian missionary who traveled the state and this is a lot of his collection. The grounds used to be Sheldon Jackson College, where I was enrolled for a short period of time, no defunct.
http://museums.alaska.gov/sheldon_jackson/sjhours.html As a side note (im most familiar with Sitka). Sitka is SMALL. The town itself is about a 15 minute brisk walk from end to end. The road system goes 7 miles north, and 7 miles south. The Fortress of the Bear is at the end of the road to the South. You could EASILY combine the Sheldon Jackson Museum -> National Historic Park (Totem Park as we call it) -> St. Michael's Cathedral -> Visit the touristy shops downtown in a day. If you move quick, you may be able to add the raptor center to this. Just like the Caribbean, every store in Alaska sells the same stuff. I'm probably going to get shot for saying that... Ketchikan: Creek Street: The old red-light part of town is now a bunch of shops, restaurants, and a museum to the worlds oldest profession. Pretty neat and a very short walk from the pier.
http://creekstreetketchikan.com/ http://www.experienceketchikan.com/creek-street-ketchikan.html Kayaking: Pretty much every port will have this in Alaska but something fun to do to get out on the water without breaking the bank.
http://www.kayakketchikan.com/ Skagway: I've never actually been to Skagway (not someplace I just want to drive 20 hours to pop in for a visit) but my parents highly raved about the White Pass & Yukon Railway. Its an old narrow gauge railway that takes you back up into the hills for beautiful views and old miner history. I would personally recommend this through the ship just for times sake. Now for expensive tours... If you want to spend money on just ONE tour (and it its a LOT of $$$$) I highly recommend doing a helicopter tour in Juneau up to the glacier with dog sledding. I would book this through the ship as weather is pretty sketchy in Southeast and if you get stuck on the ice for an hour or two waiting on a cloud to move by, you don't want to see the Wonder as she mosey's up the channel leaving you behind...though it is nice city to get stuck in. Doesn't get any more Alaskan than this. Sure, we all have helicopters, and dog sleds, live in igloos..... I have personally flown Promech Air out of Ketchikan and they were always professional.
http://www.promechair.com/ Again, I would book through the ship for anything like this just for the sake that if you're late, they wait.
With a glacier in constant motion, calving, and collapsing, being crushed by tons of ice just doesn't sound appealing! 
