We drove all the way in 2005 and took the ferry stopping at Ketchikan, Wrangall, Juneau, and Haines in 2008. The ferry for our trip with 38' of vehicle was over $1800. Unless you really want to see the Inside Passage this trip, I would not spend the money. There is a lot to see via roads. We are hoping to return this summer and priced the ferry to Sitka and could not justify $900 for us (2 passengers) and a 20' vehicle for that one stop.
The link to my 2008 blog is in my signature and there is also a 2005 blog on the Travelpod site. Take a look for some of the places we visited on the two trips.