WDW maintains quite an impressive fleet of watercraft as actual working transportation outside the parks.
The largest of these is the MK ferryboats; there are 3 of them, each named for someone significant to WDW's history. Here's a wonderful web page with details on these magnificent craft:
http://www.wcdept478.com/AbouttheFB.htm
There are also a number of launches that run around Bay Lake and the Seven Seas Lagoon, ferrying Guests among the Magic Kingdom, the 3 monorail resorts, Ft Wilderness Campground, and the Wilderness Lodge. There are at least two different sizes of motor launch, and they are color-coded with 3 different flags (blue, green, and gold, IIRC) indicating their destinations. If you're a fan of small watercraft, these launches are a fantastic way to see the MK area from the water.
You already know about the water taxis that run from Downtown Disney to the 2 Port Orleans resorts and Saratoga Springs along the Sasagoula River; these are also relaxing, slow-speed boats that take you through some pretty scenery on their routes.
My personal favorite watercraft at WDW are the Friendship Launches. The Friendships are medium-sized, enclosed, climate-controled watercraft which move Guests between Epcot's International Gateway entrance and Disney's Holywood Studios, with mutiple stops along the way at Yacht&Beach Club, the Boardwalk, and the Swan & Dolphin. They are the first watercraft I ever boarded at WDW, and remain my favorite relaxation technique for a break from the hectic pace of park touring.
There is an additional set of Friendship launches that cross the World Showcase Lagoon
inside Epcot. This is a short ride, but still nice, and it's cool to be able to see the World Showcase from the water.
I'm probably missing some, but those are the highlights of WDW watercraft.