In Paper Mario: The Thousand-Year Door, Goombella mentions having shoes. Since her sprite uses the same graphics for her feet as all the other Goombas in the game (with only a color change applied), this seems to imply that all Goombas are in fact wearing shoes. However, in Super Smash Bros. for Wii U, Goombella’s trophy shows a new design for her that adds soles to her feet, differentiating them from other Goombas and making them look more like shoes. While this design decision was most likely a coincidence, there is a chance that it could have been an attempt to clear up the above quote.
This picture was drawn by Shigeru Miyamoto during the design phase for Donkey Kong Country as a suggestion to the Rare development team that Donkey Kong should wear a tie in that game. The earlier Rare concept art visualized Donkey Kong without a tie.