According to Dave Smith, the boat officially has no name, with the short's title (a reference to the Buster Keaton film, Steamboat Bill, Jr.) instead being the name of the character Mickey plays in the short. Despite this, however, the boat has been named Steamboat Willie (or just simply "Willie") in some official Disney media, particularly where Mickey himself is not going by that name.
In the original short, the boat is first seen being steered by Mickey (nicknamed Steamboat Willie in this short), playing about in Pete's cabin as if he were the captain. Pete catches him in the act and orders him to get back down to the deck. The boat is brought to Podunk Landing where Mickey has to load a cow onto the deck. When Mickey then sees Minnie Mouse wanting to hitch a ride onto the boat, he uses the ship's crane to bring her on deck, but the goat on deck eats Minnie's fiddle and sheet music. Mickey and Minnie then spend the afternoon playing "Turkey in the Straw" with all the animals on the boat, but Pete eventually puts an end to this and makes Mickey go peel potatoes as punishment.
At the end of Aladdin and the King of Thieves, Genie exits the mouth of the giant turtle in a Steamboat Willie-like riverboat, imitating Mickey in the original short's opening scene.
In the Mickey Mouse Works episode "How to Be a Waiter", the Steamboat Willie boat is seen during Goofy's attempt at filming a silent movie. Goofy, mimicking the original's opening scene, steers an identical steamboat and ends up accidentally crashing into the original boat.
In the Mickey Mouse episode "Canned", the steamboat is amongst the Disney relics that Mickey digs up from a trash heap. It appears again in "The Scariest Story Ever: A Mickey Mouse Halloween Spooktacular".
The riverboat, explicitly called Steamboat Willie, is the subject of a comic story titled "Mickey Mouse and the River of Time" (originally published in Topolino #2243 in Italy), in which the sunken ruins of the ship turn up in a river and Mickey and Pete work to salvage the craft.
As Steamboat Willie is the subject of the first level, the very first part of the level is set on the steamboat. When Mickey comes face-to-face with his younger self from the short, Steamboat Willie Mickey bolts out of the captain's cabin.
The Steamboat Willie riverboat prominently appears in the Timeless River level. The present-day Pete steals it in order to transport the Cornerstone, but Sora and his crew manage to retake the steamboat and the stone. Later, after helping defeat his future self, the Captain Pete of the past rewards Sora and the others with a ride on his steamboat, because Mickey never showed up for work today.
In Epic Mickey, the steamboat appears in one of the game's 2D transitional stages to travel the Wasteland. Mickey travels across it in one part of the game.
In Phineas and Ferb: Across the 2nd Dimension, part of the Old-Timey Dimension has the characters visiting a version of the boat (referred to as "Willie") piloted by that dimension's counterpart of Heinz Doofenshmirtz.
At the end of the Disney's Hollywood Studios version of Fantasmic!, Mickey, in his Steamboat Willie outfit, steers the boat across the river in front of the mountain, with various Disney characters all on board the ship, dancing with golden streamers. (The original Disneyland version of the show instead uses the Mark Twain Riverboat for this scene.)