Standard Galactic Alphabet based on Latin script
Legacy
Ideas from the Deep's first royalty check from Apogee in January 1991 convinced them that they no longer needed their day jobs at Softdisk but could devote themselves full-time to their own ideas, leading to the founding of id Software in February. In the summer of 1991, id hosted a seminar for game developers with the intention of licensing the Commander Keen engine; they did so, forming the spiritual predecessor to both QuakeCon and id's standard of licensing their game engines.One of the enemies created for "Secret of the Oracle", the Dopefish, has since the game's release become one of the video game industry's biggest in-jokes, making cameo appearances in other games. The Dopefish, which Hall describes as "just a stupid green fish", is described in "Secret of the Oracle" as "the second-dumbest creature in the universe". It has appeared in dozens of other games since its initial appearance, as references, images, or the phrase "Dopefish Lives".
The Standard Galactic Alphabet, a writing system used to depict alien languages in the galaxy throughout the series, is used for textual signs and directions and was created by Tom Hall beginning with Invasion of the Vorticons as a way to pass hidden messages to players. It is a substitution cipher to the Latin alphabet, including the letters A-Z, opening and closing quotation marks, and a full stop. In 2019, it was added to the Under-ConScript Unicode Registry, using the codepoints U+EB40  to U+EB5F , and is included in the GNU Unifont CSUR extension. The Standard Galactic Alphabet also appears in the game Minecraft as the script and symbols used for its Enchanting Table.
In January 2018, John Romero and Tom Hall stated on Twitter that Billy Blaze is the grandson of Wolfenstein protagonist William "B.J." Blazkowicz and the father of Doomguy from Doom. Commander Keen himself has appeared or has been referenced in many other video games over the years, including Doom II, Duke Nukem,  Bio Menace and more recently in Doom.A number of fan-made Commander Keen games have been created since the publication of the original titles, with a fan website, the Public Commander Keen Forum, devoted to their creation, announcement, and discussion. Since the release of utilities to modify the levels and graphics in the original Keen series in 2002, more than fifty mods have been made, most of which feature Commander Keen as the protagonist. These mods include "Commander Genius", an engine, released for multiple platforms, which interprets the episodes as a "retro-evolved" game, with re-polished graphics, a multiplayer compatibility, and a level editor, ports and remakes on different platforms, and The Universe Is Toast! mod, an unofficial sequel trilogy of games.In January 2013, Tom Hall began development of Worlds of Wander, a tool for creating platform games, and the following month began a Kickstarter campaign for the tool and associated game, Secret Spaceship Club, which he described as a spiritual successor to Commander Keen. The project was unsuccessful in reaching its goal, though Hall said that he planned to continue working on it in his spare time.