Doxy is a low-dose antibiotic that happens to prevent malaria. Side effects: makes you less resistant to sun burn and if you don't take with food you'll probably puke or want to puke. I've seen a few people puke about an hour after taking it w/ no food. Bad part about Doxy is you have to take it every day. I used Doxy for my Iraq deployments with nothing more severe than an upset stomach every now and then.
Mefloquine is not an antibiotic, it's a drug used exclusively for malaria prevention. I'm on mefloquine now in Afghanistan and I like it alot more if only for the fact that you only have to take it once a week, I take it on 'mefloquine mondays' (I'm a Marine so I keep it simple). The downside to mefloquine is some people get adverse, hallucinatory reactions to it. In fact the British troops/Marines I'm with aren't allowed to take mefloquine for more than 4 months at a time due to what they have found to be 'permanent, negative effects' on the body. They didn't know what these 'effects' were. Just that it's tough on the body.
Right now I'm going on month 4 taking mefloquine along w/ vitamins, creatine, protein supplements and feel as fine as I can in this environment. I actually enjoy the dreams associated w/ a nighttime dose of ZMA and mefloquine.