Walt Disney World boat transportation is concentrated around three areas: Bay Lake & The Seven Seas Lagoon, the Epcot Resorts and Studios, and the Downtwon Disney resort area.
Boats will still take you from Port Orleans (French Quarter), Port Orleans Riverside (formerly Dixie Landings), and Old Key West to/from Downtown Disney.
Another boat route is from the Studios, to Swan/Dolphin, Yacht & Beach Club Resorts, Boardwalk, and finally Epcot's International Gateway entrance - in that order (reverse the sequence to go from Epcot to the Studios).
Over on Bay Lake, boats operate from Fort Wilderness and Wilderness Lodge to the Contemporary; a seperate boat goes from the Lodge and campground to the Magic Kingdom. On the Seven Seas Lagoon, you of course have the MK to TTC ferryboat, but also smaller craft that run between the Magic Kingdom and The Grand Floridian and the Polynesian Resort.
Caribbean Beach, Coronado Springs, Animal Kingdom Lodge, and all of the value resorts are effectively landlocked - no boat service (except small rental craft around any resort lakes, where they exist).