Flagyl and biaxin worked well for my.. doxy, not so much. Plaquenil & Z-Pak is a newer protocol docs are using (well at least up here in canada, everyone knows how ignorant the canadian health care system is towrd lyme).. good luck!
Based on what I've read about patient experiences, amoxicillin is a popular choice for treating Lyme, especially in younger patients. Doxycycline is also widely used in treating Lyme.
I've taken neither of those two. Depending on if/what co-infections the patient has, other meds/combinations can be effective. I've been on several different antibiotics, including minocylcine, azithromycin, and factive.