Short answer: WebM for Chrome, Firefox, Edge and OBS; ProRes 4444 for editing software; HEVC with alpha for Safari and iOS; PNG sequences for game engines and animation tools.

By destination

DestinationUseAvoidDetails
Chrome, Firefox, EdgeWebM (VP9 alpha)H.264 MP4Website guide
Safari, iPhone, iPadHEVC with alpha, or a PNG stillWebM (alpha ignored)Safari guide
OBS overlays and stingersWebM (VP9 alpha)Chroma key on a transparent fileOBS guide
Premiere Pro, After EffectsProRes 4444WebMEditors guide
DaVinci Resolve, Final Cut ProProRes 4444WebMEditors guide
Game engines, sprite toolsPNG sequenceAny lossy videoVideo to PNG
Anything, as a check—Plain H.264 MP4: no alphaMP4 guide

What this is based on

We tested the file formats themselves: every export and conversion here is decoded and checked for real transparent pixels, and transparent WebM playback in Chrome. The browser and application rows follow each vendor’s documentation and long-standing behaviour at the time of writing; versions change, so test in the exact app you deliver to.