Have any operational aircraft ever used over wing fuel tanks?
Early aircraft designs used gravity feed to supply the engines with fuel. All those designs had their tanks located above the wing, and in biplanes in the center of the upper wing. The picture below (source) shows an Etrich Taube with the cylindric fuel tank mounted above the fuselage.



The next application of overwing tanks were "Doppelreiter" fuel tanks (slipper fuel tanks) which were used on some German fighter airplanes in WW II. They were mounted above and behind the wing, and to everyone's surprise they had little impact on the top speed of the airplanes, and in case of the Me-309 helped to increase it slightly. They were the first practical application of Küchemann carrots and worked much like the flap track fairings of today's airliners.



FW-190 A with Doppelreiter tanks.