First of all, the tetanus shot doesn't hurt. Some people get some pain and stiffness several hours later, but I tell my patients to drop down and knock out 10 pushups to work it into the muscle and they won't have any problem.
As far as the Meningococcal vaccine, I've not heard of any side effects among my Soldiers aside from a mild headache, which is easily treated with motrin.
HPV was said to sting a bit, but that is because it used to be given sub cutaneously (SC). Any vaccine given SC is going to sting because that area is highly innervated. But anymore, it's given intermuscularly (IM), right into the muscle, and stings a whole lot less. Still, there may be a teeny bit of burning at the vaccine site for a minute or so.
All of these vaccines are quick, administered IM with teeny tiny needles. The dose is 1ml/cc or less, which is a very tiny amount. Let your son know that it will be over quickly, and, if you have an ipod or mp3 player with headphones, have him put on some music nice and loud. The music actually makes the vaccinations hurt less because his nervous system is focused on what he's hearing. Kind of a neat trick I'd suggest to anyone with nervous kiddoes. Also, if he's a bit skinny, like my own boys, ask that the vaccines be administered in his thighs instead of his skinny little arms.
ETA: Sigh. There's always someone who will give completely incorrect advice. Please know that HPV, though very treatable, is NOT curable. Once you have HPV, you have it for life.