We used the ferry system for our return trip from Alaska in 2015. We took the ferry from Haines to Juneau, stayed a few days in Juneau, then took a different ship from Juneau to Bellingham, Washington. The later segment took four overnights, thus we booked a cabin as well. It was a wonderful experience, great employees, good food, and stops that allowed us to visit Sitka and Ketchikan for several hours. More time in those places would have been nice, but our schedule was constrained by other reasons. Agree with PA12DRVR that SE Alaska is a different experience.
We booked early Spring for the Ferry. Reminder, the fee is based on the overall length of your rig (and toad), and whether or not you want a cabin. (Some folks just pitch a tent on the aft deck of the ship). In general, we would recommend the ferry to anyone considering it.