The Quantum Disruptor can hurt Superman - Stop the Presses
Another Kryptonian using a Dre (not sure of the spelling) can hurt Superman - (In Battleground Earth, Clark hurt Nor this way)
Dr. Doodson's device, the youth machine, caused Superman to lose some years so one could assume it could hurt Superman if used for long enough - Brutal Youth
A very large concentrated dose of magnetic charges could hurt Superman - at least Deathstroke was able to do it in Bob and Carol and Lois and Clark.
Those are the ones I can think of at the moment.
