My 16 year old daughter has a stiff neck, headache, ear ache, throat ache, and occasional stomach pains. What could this be? Should I be concerned?

Stiff neck, headache. Definitely sounds like she needs an evaluation. Does she have fever? If she has changes in altertness then it requires emergent evaluation.
Virus? This sounds like a virus, and may respond to tylenol (acetaminophen) or motrin, but if your daughter has high fevers and stiff neck, especially if she is not acting normally, she should be checked for meningitis (an infection of the lining of the brain and spinal cord).