Malaria medication
As Blinkz says, it depends a lot on the type of medication, which in turn depends on where you are going. There is a huge variation in resistance to medication between malarious areas.
Many jurisdictions (notably militaries) do not allow flying on Lariam (mefloquine) because of the side effects. These can include hallucinations, and other neuropsychiatric effects.
The best advice is to see an AME with an interest in travel medicine (many of them do) to get the best medicine for the area that is still compatible with flying.
Cheers,
BM