Sulfonic acids, from which sulfonamides would presumably be biosynthesised, are themselves quite unusual in natural products. One which is common is taurine, 2-aminoethanesulfonic acid H2NCH2CH2SO3H. I have not heard of its amide being found in Nature.
To find unusual structures in biological molecules, search databases of fungal and bacterial products. You will find some weird structures indeed. Plants don't do badly either. They probably stole the genes responsible from bacteria and fungi that used to live inside them (shelanachium's pet theory!)