Scar, hair color, eye color, skin color, disability.
^ ... but what about in a fantasy or high tech world where those things can be changed??
Fingerprints might work in a fantasy or modern world ... if you're human ... not sure about nonhumans though.
... but if you're going for just the 'Joe Average' villager in a medieval setting ... I think I read somewhere like in 'Medieval Demographics Made Easy', most villages tended to be around 100-150 people. And most people stayed in the same place nearly their whole lives. In this situation, nobody needs 'proof' because you are a known thing. Someone's gonna say, "hey I remember when that boy tried to kiss my daughter and I slapped him silly". Lots of little things like "everybody knows everybody else and their business".
For the most part this works ... again, for smaller communities. Even in moderate sized towns, there's always someone around who can vouch for you. Hmm, maybe the above "that kid tried to kiss my little girl" also works in towns too. Or cities.
In adventure type novels where characters obviously go beyond their comfort zone, simple recognition goes out the window ... unless you're traveling with others who also are a known thing at your destination. Depends upon how (in)famous you want your characters to be.
But in reality, if you're dealing in 'identification systems' then be aware, you have to also figure out how such a thing could also backfire or be misused or just plain not be as secure as originally intended. Even if you write in such a thing, at some point you'll get a reader saying "hey why did this work when I don't think it should" or "why not just do __".
Nothing gives better identification than seeing something happen firsthand, or secondhand by word of mouth from someone who has firsthand knowledge. Nothing trumps those in a community of any size. But I do realize the question also becomes the validity of the other person vouching for you ... aaaaaaahh it's a crazy rabbit hole, don't go down that way....
Nothing is perfect, nothing is beyond being corrupted or misused (either IRL or in fiction). In fact this could be part of a plot, to lay out to your readers you as a writer are also considering these things (as well as your characters should).