Since there is already a list of level hacks, we need to show some love to the improvement hacks also!
Castlevania II: Simon's Quest

Castlevania II Annoyance Fixes - tkempkes
3 ips files that remove the false floors, horrible night dialog and doubles heart values.
Link
Chrono Trigger

Chrono Trigger Bugfix - ManuLowe
Fixes a lot of the text to make the game make more sense. Helped me out a lot.
Link
F-Zero

F-Zero Tracks Unlocked - smkdan
Allows all of the tracks to be unlocked from the start.
Link
Final Fantasy

Final Facelift - Goongyae
Great improve that retranslates and restores the game to what it should have been.
Link

Final Fantasy++ - Grond
Redoes the graphics and adds new maps, while also correcting the class system.
Link

Final Fantasy I-4 - Egadd
Based off of Final Facelift, this improvement redoes most of the spells and includes a 6th spell name slot.
Link
Final Fantasy IV

FF2 Modernization Hack - SirRob
Similar to Goongyae and my hack, this changes armor, spell, weapon and other names.
Link

FF4 Magic Plus - Deathlike2
Adds usability to Sight and Dispel.
Link
Kirby's Adventure

Kirby's Adventure UFO Fix - Dizzy9
Lets you keep UFO after a level is done.
Link
Ogre Battle: March of the Black Queen

Ogre Battle Army Balancing Mod - FinS
Too much for me to describe. In his words
Originally posted by FinSThis mod makes the previously undervalued units useful and adds a new class to the witch line which she can promote to at level 15 then she can use an undead ring to become a sorceress. The mage now promotes with an undead staff. Many attacks have been changed to make the game more enjoyable. Vampyre now uses an evil ring attack, the top dragons have three area of effects from the back row, the Cockatris keeps the Gryphon’s gale and has the petrify up front. All top level beasts now have 4 front row attacks and their resistances have been increased. Giants and Golems now have a normal chain of promotion just like the other characters. Evil ones, Muses, Beast Masters, Dragoners, Dragon Masters and Tigermen all get an extra attack up front. All four lords have been improved. Generals and Dragoons have 3 back row attacks because they are g d heros man. The only reduction is to the Lich which has 2 for balance, he is still the most powerful character in game. The goal is to make any character good enough to be valuable at the end of the game. I tried not to adjust too many stats or change anything unnecessarily but only to improve the characters in need. Included is a reference guide with all the important stats.
Link

Ogre Battle v.1.02 - red_bird
Tweaks genders, job trees and stat growth.
Link
Pokemon

Pokemon Red: Dark and Steel Types - Koolboyman
Overhauls the matchup system to include Dark and Steel types.
Link
Sonic 3 & Knuckles

Knuckles and Tails - SonicHalloween
Has Tails follow Knuckles around like he does Sonic.
Link
Sonic the Hedgehog

Sonic 1 Spindash - Esrael
Adds Spindashing.
Link
Sonic the Hedgehog 2

Sonic 2 Delta II - Esrael
The Sonic 2 version of SMW Beta. This includes all of the original Zones, along with adding Sonic 3 graphics, a ring counter showing you how many remain, and Knuckles! A must have.
Link
Super Mario Bros.

Super Mario Bros. DX - flamepanther
Overhauls all of the graphics to reflect SMB3 standards.
Link
Super Mario World

Super Mario World: Graphics Hack - peter_ac
Like DX, replaces all of the graphics to SMB3 GFX.
Link
Feel free to add more to the list!
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