In 2012 we spent roughly the month of June exploring SE Alaska using the AMHS. Before the trip, I spent a bunch of time on the AMHS website reserving a series of independent, one day, ferry hops between the port towns where we then spent a few days exploring (class C RV towing a Jeep). The legs were booked to allow for easy daylight sailings.
Our itinerary:
Prince Rupert -> Ketchikan (5 nights)
Ketchikan -> Wrangell (7 nights)
Wrangell -> Petersberg (3 nights)
Petersberg -> Juneau (2 nights)
Juneau -> Sitka (fast ferry, 6 nights)
Sitka -> Juneau (fast ferry, 2 nights)
Juneau -> Gustavus (left RV in Juneau, 3 nights at Glacier Bay Lodge)
Gustavus -> Juneau (3 nights)
Juneau -> Haines (7 nights)