What is the best medication for allergies?

There are numerous medications available for the treatment of allergy symptoms. In general, a medication that works particularly well for one person may not work for another, especially when the allergy symptoms are different. That being said, there has been numerous studies published comparing the effects of antihistamines, nasal steroids, and antileukotriene medications (such as Singulair).
Nasal steroid sprays, such as Flonase (fluticasone), Nasonex (mometasone) and various others, show the best efficacy in treating allergic rhinitis. The downside to these medications is that for best effect, they need to be used regularly. And, while many people don't like the idea of spraying a medicine in their nose, the benefit of symptom relief is worth the trouble. Nasal sprays can also help eye allergies, although studies on this effect are inconsistent.
Anthistamines, such as Zyrtec (cetirizine), Allegra (fexofenadine) and Clarinex (desloratadine), are also very effective therapies for the treatment of allergies. These medications tend to work quite well on an as-needed basis, with an improvement of symptoms within an hour or two of taking the medication. Oral antihistamines also work quite well for the treatment of eye allergies. And, of course, there's nothing easier than swallowing a pill to treat your allergies.
Singulair (montelukast) is a medication that works similar to an antihistamine, but blocks another chemical mediator of allergies, called leukotrienes. This medication is indicated for the treatment of allergies and asthma, but is not a great medication for either. I tend to prescribe Singulair in conjunction with another medication, such as an antihistamine.