Jeter leads off with single
Gwynn hits into fielder's choice
Mauer walks
Musial hits routine fly to right, idiot drops it...

bases loaded, one out
Clemente singles, runners advance one base - bases still loaded, 1 run scores
next two guys fly out, not deep enough for anyone to tag and score

1 run

had the idiot right fielder caught the ball, it would have been runners on 1st and 2nd, 2 outs
Clemente hits single, runners advance one base - bases loaded, but no runs
next guy flies out, inning over

0 runs

The runner that scored could have still scored from second on Clemente single whether he was on 2nd or 3rd, maybe.

Perhaps, but the guy who actually was on 2B held at 3rd...

MLB rule 10.16 covers earned runs.  By my reading of that rule, although this exact situation is not covered explicitly, the run should be unearned. 

The critical phrase to me is this one (in the opening paragraph of 10.16): "giving the benefit of the doubt always to the pitcher in determining which bases would have been reached by runners had there been errorless play."

It seems to me that while the runner on 2nd could have scored on Clemente's single, the phrase above implies we should give the pitcher the benefit of the doubt and only assume 1 base advanced.  Hence, unearned run.

I think it is up to the official scorer whether he thinks the runner would have scored from second.  Maybe the guy on 3rd is a faster runner than the runner on 2nd.