Best is a bad word unless I say best at what. For applying a patch you already downloaded, the browser engine on the home page is the one I open, because it needs no install and it prints hashes. It is Rom Patcher JS, MIT licensed, pinned here at commit 4f17297. I am not awarding it a score. patchmyrom.com is another browser tool with format pages and checkers. rompatcher.app calls itself the official online patcher and lists base ROM names without hashes. I would rather show a hash than a crown.
The split by job, from the tools I actually checked: A native Mac workflow goes to MultiPatch 2.0. Android, if you want an app, goes to UniPatcher 0.19, not to a random APK. Large DS, GameCube, and PS2 images go to Delta Patcher 3.1.6 or xdelta3. IPS-only creation on Windows goes to Lunar IPS 1.03. UPS creation with an offset list goes to NUPS 1.4. BPS creation goes to Floating IPS. Those are different winners. A table that sorts them into one ranking would be a story.
I did not run patchmyrom's compatibility checker as a product test. I read the site structure. Until that test exists I will not claim this hash hint is a better checker. I will claim the hashes on the FireRed, Emerald, and Mario 64 pages are the ones the pret and decomp repositories publish, which you can compare yourself.
Related pages: the tools index for versions, the safety page for installers, and the home patcher for the no-install path. If a listicle gives you one download button, leave it.