The FAA does not approve medications, per se. Any given medication must be considered in conjunction with the reason for which it is taken. A medication of itself may have no adverse side affects in the general population, but in most cases the condition for which the medication is taken is a grounding item.
An over the counter medication such as sudafed may be acceptable, or a certain version of the drug may be acceptable. However, the condition for which it's taken, nasal congestion for example, may be very dangerous in flight. You may alleviate the symptomatic presentation of the condition, but not necessarily the condition. In other words, you'll feel fine, up until your sinus implodes while in a descent.
(I can tell you from personal experience that the pain is exquisite, and unbelievable from this particular condition, having been hospitalized on one occasion, and made deaf for a month on another).
Follow the following link for some general information on medications. Explore the links on this site, too. There is some good information on the subject.
I agree with Avbug. However, you can use certain prescription meds and still fly. Check out the website that Avbug recommended. You can also call AOPA; it gives excellent, confidential advice. Do NOT ask your friendly AME. The AME is the FAA's industrial physician and, as such, does not have your interests in mind.