And if you used join you wouldn't have to worry about incorrect trailing seperators.

$graph .=
   join( ", \\\n",
          map qq{"tmp/$random.dat" using 1:$_ title '$inputs[ $_ - 2 ]
+' with lines}, 
            2..$#inputs+2 );
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Update: And of course you'd append a "\n" on the end of that otherwise you're right back where you were stuck before. %/