Seems to me you could poison him. He's invulnerable - ie, his skin can't be penetrated, scraped or burned, but I imagine his insides are just as vulnerable as the next person's. All you have to do is find the chemical(s) that are toxic to Kryptonians. A carefully orchestrated series of tests would do the trick (ie, spike his food <g>).
Also, you can give him a virus. We saw as much in the series.
Yvonne
