49. Alien Soldier (Treasure, 1995)
48. Thief Gold (Looking Glass Studios, 1998)
Metal Gear may have popularized the genre, but Looking Glass's Thief is without a doubt my favorite stealth game franchise, primarily because it carries the tension of the genre so well - you were sticking to shadows every step of the way, glancing over your shoulder for enemies, and using any tricks or hidden passages you could find to avoid being seen (or make a quick escape if you were). The grim fantasy setting and eerie architecture only added to the mood, as well as giving you some unique and fantastic tools for the job - from moss arrows (quieting your footsteps on metal and stone floors) to rope arrows to flash bombs and gas mines, you had plenty of options to accommodate your particular gameplay style. Add multiple difficulty settings on top, each with their own mission objectives, and you have a game with plenty of replay value as well. To say nothing of some of the brilliant fan-made missions and level packs out there.
47. Ultima Underworld: The Stygian Abyss (Blue Sky Productions, 1992)
A game that was built from the ground up to not just be a more realistic kind of puzzle-driven dungeon crawler, but a full blown life simulation too. To that end, you had skills not just oriented around combat and spellcasting, but for swimming, conversing, identifying items and bartering with NPCs among many others. It had a lighting system and rudimentary physics for platforming, letting objects bounce off of walls (and activate switches) and no single set solution for most puzzles, letting the player take an innovative approach to figuring out the game's mysteries. Downright mind-blowing stuff for 1992, and the influence it's had on the industry since is immeasurable. inspiring games like Elder Scrolls, Half-Life 2, Deus Ex, and numerous others. It's a bit clumsy and awkwardly slow to play today, but it's nevertheless a great game and an important building block for gaming as a whole.
46. Danganronpa (Tetralogy) (Spike Chunsoft, 2014-2017)
45. Ultima IV: Quest of the Avatar (Origin Systems, 1985)
44. Legend of Zelda: Majora's Mask 3D (Nintendo, 2015)
43. Final Fantasy VII (Squaresoft, 1997)
41. Deltarune (Toby Fox, 2018)