Your strings are quoted wrong, your second double quote after on click = terminates the string, I havent tested my soloution but you need something like (below)
You need to escape double qoutes if it is literally part of the string
echo "<tr><td colspan ='2'><center><input type="submit" value="Reply" onClick='window.open(\"post_reply.php?cid=$cid&tid=$tid\")' />";
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solved Button not doing anything on click. How come? [duplicate]