READ and follow label directions for use of medication.
If the label warns of side-effects, do not fly until twice the recommended dosing interval has passed. So, if the label says "take every 4-6 hours," then wait at least 12 hours to fly.
Remember, the condition you are treating may be as disqualifying as the medication.
When in doubt, ask your physician or Aviation Medical Examiner for advice.
As a pilot, you are responsible for your own personal "pre-flight." Be wary of any illness that requires medicine to make you feel better.
If an illness is serious enough to require medication, it is also serious enough to prevent you from flying.
Do not fly if you have a cold - changes in atmospheric pressures with changes in altitude could cause serious ear and sinus problems.
Avoid mixing decongestants and caffeine.
Beware of medications that use alcohol as a base for the ingredients.
http://flysafe.faa.gov/Flysafe/Library/Airman%20Medical%20Info/OTC%20Medicine.htm