https://kosmfit.itch.io/swatchsmith
Swatchsmith recolours every PNG in a folder at once. Tick the colours to change, then map a whole ramp to a new palette (Lospec .hex, GIMP .gpl, JASC .pal and paint.net palettes, or a PNG palette image, load directly). Lock colours like outlines and eyes, and export as many variants as you need in one ZIP.
New in 1.1: paint a region to recolour only part of a sprite (say, a helmet but not the body armour, when both use the same colours). The export also comes with a palette lookup texture and ready-made Godot 4 and GLSL shaders for runtime palette swaps.
It's a single HTML file that runs offline in your browser on Windows, macOS and Linux, with no install and no uploads. $4.99. You can try it free in your browser first (3 sprites, 1 variant): https://kosmfit.github.io/swatchsmith-demo/
Sprites in the GIF: Tiny Dungeon by Kenney (CC0).
AI disclosure: the code and page text were made with help from generative AI (details on the page). The tool itself contains no AI and only recolours your own pixels.