List of Famicom Disk System Games which Write to Disk

[Great Hierophant]

The Famicom Disk System offered non-volatile storage to any game released for the system.  Not all games took advantage of its capabilities, sometimes because they were ports from a cartridge, saving would make the game too easy or it did not fit into the game's design.  Many games did support saving something to disk, whether it was progress in the game, the levels finished, the number of times the game was completed, high scores or contest data intended for the Disk-Fax service.

Licensed Games :

Adian no Tsue
Akumajou Dracula
Akuu Senki Raijin
All Night Nippon Super Mario Brothers
Apple Town Monogatari - Little Computer People
Aspic - Majaou no Noroi
Big Challenge! Go! Go! Bowling
Big Challenge! Juudou Senshuken
Breeder
Bubble Bobble
Chitei Tairiku Ordola
Cleopatra no Mahou
Clu Clu Land
Cocona World
Dandy - Zeuon no Fukkatsu
Dead Zone
Dirty Pair - Project Eden
Doremikko
Dr. Chaos - Jigoku no Tobira
Dracula II - Noroi no Fuuin
Egger Land
Egger Land - Souzou e no Tabidachi
Electrician
Esper Dream
Exciting Baseball
Exciting Billiard
Exciting Soccer - Konami Cup
Fairytale
Famicom Grand Prix - F1 Race
Famicom Grand Prix II - 3D Hot Rally
Famicom Mukashibanashi - Shin Onigashima
Famicom Mukashibanashi - Yuuyuuki
Famicom Tantei Club - Kieta Koukeisha
Famicom Tantei Club Part II - Ushiro ni Tatsu Shoujo
Family Composer
Famimaga Disk Vol. 1 - Hong Kong
Famimaga Disk Vol. 2 - Panic Space
Famimaga Disk Vol. 3 - All 1
Famimaga Disk Vol. 4 - Clox
Famimaga Disk Vol. 5 - Puyo Puyo
Famimaga Disk Vol. 6 - Janken Disk Jou
Fire Bam
German Tanteidan MarinGumi - Maruhi Jigomar Sousa File
Ginga Denshou - Galaxy Odyssey
Golf - Japan Course
Golf - Japan Course Prize Card
Golf - Special Course Prize Card
Golf - US Course
Hao-kun no Fushigi na Tabi
Hikari Shinwa - Palthena no Kagami
Hikaru Genji - Roller Panic
I Am a Teacher - Teami no Kiso
Idol Hotline - Nakayama Miho no Tokimeki High School
Jikai Shounen Met Mag
Kaettekita Mario Brothers
Kalin no Tsurugi
Kamen Rider Black - Taiketsu Shadow Moon
Kieta Princess
Knight Lore - Majou no Ookami Otoko
Knight Move
Link no Bouken - The Legend of Zelda 2
Lutter
Madou Senki - Deep Dungeon
Maerchen Veil
Meikyuu Jiin Dababa
Metroid
Monitor Puzzle Kineko, The - Kinetic Connection
Monitor Puzzle Kineko, The - Kinetic Connection II
Monty on the Run - Monty no Doki Doki Dai Dassou
Namida no Soukoban Special
Nankin no Adventure
Nazo no Kabe - Block Kuzushi
Nazo no Murasamejou
Nazoler Land - Dainigou
Nazoler Land Special!! - Quiz Ou wo Sagase
Neunzehn - 19
Omoikkiri Tanteidan HaadoGumi - Matenrou no Chousenjou
Otocky
Pachinko Grand Prix
Patlabor - The Mobile Police - Daini Shoutai Shutsudou seyo!
Pro Golfer Saru - Kage no Tournament
Professional Mahjong Gokuu
Putt Putt Golf
Puzzle Boys
Radical Bomber!! Jirai-kun
Reflect World
Relics - Ankoku Yousai
Replicart
Risa no Yousei Densetsu
Samurai Sword
Santa Claus no Takarabako
SD Gundam World - Gachapon Senshi - Scramble Wars
SD Gundam World - Gachapon Senshi - Scramble Wars - Map Collection
Section-Z
Silviana - Ai Ippai no Little Angel
Suishou no Dragon
Super Lode Runner
Super Lode Runner II
Super Mario Brothers 2
Tantei Jinguuji Saburou - Kiken na Futari
Time Twist - Rekishi no Katasumi de...
Titanic Mystery - Ao no Senritsu
Tooyama no Kinsan Space Chou - Mr. Gold
Topple Zip
Transformers - The Headmasters
Ultraman - Kaijuu Teikoku no Gyakushuu
Ultraman 2 - Shutsugeki Katokutai
Ultraman Club - Chikyuu Dakkan Sakusen
Vs. Excitebike
Wardner no Mori
Winter Games
Wrecking Crew
Yume Koujou Doki Doki Panic
Yuu Maze
Yuushi no Monshou - Deep Dungeon
Zelda no Densetsu - The Hyrule Fantasy

Unlicensed Games :

Bodycon Quest I - Abakareshi Musumetachi
Lipstick #1 - Lolita Hen
Lipstick #2 - Joshi Gakusei Hen
Lipstick #3 - OL Hen
Lipstick #4 - Hakui no Tenshi Hen
Lipstick #5 - Stewardess Hen

My list should be complete, but the language barrier at times made it difficult to determine whether a game actually saved, even with the help of FDS Explorer.  So if anyone sees an omission or a false positive, let me know and I can investigate further and revise the list.

[P]

Great list! There's surprisingly few. According to Wikipedia there should be 200 licensed Disk System games and this list has only a little over half of that (though Wikipedia also lists Eggerland Souzou e no Tabidachi twice for some reason, once as unreleased which is weird).

[Preki]

Electrician saves hi-scores to the disk, would be nice if it would save your progress too, although it's by all means an arcade-style game.

[adori_12]

Great job! I'm a sucker for Famicom lists. 

However, you forgot to add Seiken Psycho Calibur: Maju no Mori Densetsu.
It's a Zelda-like game which allows you to save your progress, up to 3 save files.