In my opinion:
If memory serves me right (as I played the game a while back), Shantae and the Pirate’s Curse’s intro stage acts as a tutorial, but it’s so seamless to gameplay and story that it barely feels like so. Iirc, also same for Valkyria Chronicles 4’s first mission.
And that I remember better due to playing relatively recently, Final Fantasy VI and Catherine’s tutorials are well integrated to their games’ specific flows, the former being a series of NPCs you talk to, something you already do a lot in the game, and the latter being quick, straight to the point and given like it is a normal part of the narration and the increasingly frenetic (for a puzzler) gameplay.
And also if memory serves me right, Dirge of Cerberus and Outlive both have optional missions in their main menus that act as tutorials, that don’t feel like a chore, and that if you ignore them, the game is still sufficiently manageable.
KDE’s Dolphin + Konsole’s integration to Dolphin is great for seamlessly managing files with an UI and terminal hybrid.
Though closed source (overly dramatic music plays), the text editor Sublime Text works great, and at least with major version 3 (last I checked it was in version 4), it can be converted to AppImage without major issues (at worst, paths with spaces have issues).
Firejail is great for starting specific programs offline.
Newsboat is the best RSS feed reader I could find for Linux, specifically due to, with its inbuilt macros, I can set it up to open in new tabs several posts from a comically large amount of feeds.