Internet person SethBling has successfully coded Flappy Bird inside of Super Mario World, by hand, by playing SMW on actual Super Nintendo hardware in a very peculiar way. Full hour-long process. SethBling's notes for the process. (Previously, on MetaFilter: injecting code in SMW; glitching SMW.)
In Super Mario World, if you make the right series of moves with the right game objects, you can cause the game to execute arbitrary code. A particularly delightful use of this feature was recently shown by Masterjun, a tool-assisted speedrun enthusiast. He unveiled the speedrun to the world using an unmodified game cartridge and a Super Nintendo Entertainment System with eight controllers connected through a multitap system at the Awesome Games Done Quick 2014 event. Hack A Day explains the technique. Masterjun explains it in more detail.
With the release of Super Mario Galaxy on Wii, now is a perfect time to look back at the History of the Super Mario Brothers.
Metroid Cubed...Squared! It was linked a couple years ago, but since then the site has undergone a major overhaul and added a bunch of cool stuff. [Flash Warning] In addition to the now classic voxel 2.5D conversion of Metroid (playable and interesting), there is now a robust Metroid world-editor, a Marble Madness-like prototype using the voxel engine, a StarFox level editor and model viewer (Spoiler: gfx not as good as you remember), and numerous others worth checking out: Hyrule Planetoids (comme Le Petit Prince) and a OpenGL Zelda room viewer, a Mario 64 Explorer, and numerous Super Mario Bros demos. It's all quite useless/amazing.