I'm a budget traveler so I get you....
Juneau- On my first trip to Juneau I took the city bus to the fish hatchery, and later took the Glacier Express to Mendenhall did a bit of walking around, and ate salmon. That whole day was like less than $60. Unless you have your heart set on certain vendors, don't prebook as there are a ton of kiosks in Juneau of people trying to sell you tickets to different things like whale watching, rafting, helicopter rides, and tours. On my 2nd trip I did the canoe trip to Mendenhall since I regretted not doing it. While it was fun, you could just hike to Mendenhall. I would have done it, but I'm lazy. On my next trip I plan to just go to Gold Creek for the all you can eat salmon (RC has it listed at $47 which is cheaper than booking direct as the going rate is $56), and walk around Cope Park which is a nice walk from what I hear from the pier. I'd consider doing the Mt. Roberts Tram, but so many of Alaska's activities are based on the weather in my experience so if the weather is nice and not overcast , maybe book the tram.
Skagway- First trip did a ghost tour which was a lot of fun and didn't cost a lot. Ended the day by going on the train to White Pass. Definitely not cheap, but I did the cheaper option ($130) which was shorter but enough for me. On my 2nd trip I did the 6 hour bus version of the train ride but went into Canada. Tour was called Yukon Klondike Adventure by Bus through Chilkoot Charters & Tours and cost me $95. Included an all you can eat lunch which was really good. They have a half bus/half rail option as well. Anyway was a long day but fun. If I did it again I'd just eat on the ship, walk around town, and if possible rent a car.
sitka- Never been but will be going on my next trip. I plan to do the Raptor Center, Fortress of the Bear, and the cathedral. From what I read their are cheap shuttle buses.Eat on ship to save $$.
Victoria- same as above. You don't get a lot of time in Victoria so my only plan is to go to the gardens.If there were more time I would have added on whale watching but I could skip it (done my fair share of whale watching...only want to see killer whales).
In any case, don't book direct through the cruise unless you have to.
You also can rent a car but when I looked into it, they were always sold out (I did check for cancellations). Not a big deal. I enjoyed getting a tour hearing information.