Bordetella is resistant to Amoxicillin, but seems to be sensitive to just about every other antibiotic. The most commonly used are Clavamox and Baytril, either in conjunction, or alternating weeks. The most important thing–treatment must be continued for at least 14 days! Some veterinarians recommend a 21 day treatment period.
Other drugs used: Chloromycetin, Kanamycin, Gentamicin (2mg/lb up to 4 weeks old, 4mg/lb after), Tetracycline, Cephalasporine (at 4x the normal dose), Doxycycline (50mg daily per adult cat), Antirobe, Cephalothin, Trimeth-sulfa, Primaxin (the most effective, but also the most expensive. Dose is given 3x/day by IM injection). A caution–Gentamicin should be used judiciously in kittens, because it can cause permanent kidney damage in some cats.
Another point–if one cat in the household has been diagnosed, all cats have been exposed and must be treated for the full 14-21 days, or you will experience repeated outbreaks of more and more resistant strains.
Even after a full scale treatment, breeders have reported re-breaks that required isolation and additional treatment.