Software with Sprite Editor

GameMaker is a 2D-first engine with a built-in sprite editor and room editor, used by many of the best known pixel art games.

Novaboard runs in the browser and as a desktop app, with layers, animation and effects.

PICO-8 bundles a code editor, sprite editor, map editor, sound effect editor and tracker into one tiny virtual machine with strict limits that keep games small and finishable.

TIC-80 is an open source fantasy console in the PICO-8 mould with a larger screen, several scripting languages, and built-in sprite, map, sound and music editors.

Unity is a general-purpose game engine with a well-worn 2D pipeline: a sprite editor and atlas packer, a tilemap system with rule tiles, 2D lights and shadows, and a large asset store. It is heavier than the dedicated 2D engines, and in return it goes anywhere.