Process of elimination; couple of ideas. Say the song is in G. Wait for the G chord to come around. Elwood made a good suggestion above - "cowboy D chord" - but shift it up the neck to G. Just the top three strings - does it sound OK? Then one of the other strings is the culprit (but that's rarely the case). So, let's assume that G chord on strings 1, 2 and 3 sounds a little bit "off". Now you know it's 1, 2, or 3. Next chord (or whenever), mute the first string. Then mute the second string. You're gonna find it. Once you know which string, It's almost always gonna be flat, (and BTW it's almost always gonna be one of the strings that you bend).
And after 60 years you don't have to be told this, but nevertheless - just go to youtube and look at some of the old C,S,N or C,S,N,Y live gigs - hear how badly Stills' guitar got out of tune and he just kept singin' like an angel as if nothin' was wrong (bad foldback in those days so he probably couldn't hear himself anyway) - my point is that even Superstars sometimes get out of tune.