I always take a Rx medication called Entex when I fly (unless I'm in great helth and it's less than a 2 hour flight) and drink at least 6 oz of water per hour that I fly as I tend to get sinus infections. This has helped a lot. (And, yes, I always ask for an aisle seat, as I'll be making a few pit stops due to all that water!)

Don't discount the need to take water with a lot of these medications (advil, etc.) Also, cut down on things that will dehydrate you - salty food, coffee, alcohol.

When things get really bad, a cup of tea or hot water with lemon or even a hot compress can make a big difference in opening up the sinuses and can be done on board. (If it's a long 7 hour+ flight, I often throw an old, clean washcloth in my carry-on for the hot compress.) It may seem slightly strange to non-frequent flyers, but it's better than a burst ear drum or intense pain or another dose of antibiotics.

By the way, if the pain persists, you deifinitely need to go to the doctor. You also won't necessarily feel bad anywhere else - no fever or flu. Since it'll take a few days for a bad infection to clear up, don't hesitate, as it could be worse on the return flight!