Can breathing in helium (from balloons for example) cause damage to the throat in the long term?
When we speak, our vocal cords vibrate to the air. Helium makes them vibrate a lot faster (that's what makes the funny sound of your voice after inhaling helium), because its atoms are a lot lighter than nitrogen and oxygen atoms. Obviously, lighter atoms, can travel faster. This faster vibrations are unusual to the cords and they can cause sore throat or even strong throat ache. After you stop inhaling the gas, things should get back to normal, especially if the inhalation really is infrequent. 

Breathing helium balloons at parties is a very dangerous fun activity, because it replaces the oxygen and this could lead to hypoxia - a condition when tissues can't get enough oxygen one reason or another. In some cases, this could even be fatal. 

Even though inhaling of pure helium is dangerous, in submarines, divers breathe a mixture of nitrogen, oxygen and helium as helium is better under higher pressures. At these depths the low density of helium is found to considerably reduce the effort of breathing. Divers often have problems with dry throat and constant thirst due to the need of more oxygen. At least, inhaling helium, when it's mixed with oxygen, is far less harmful than breathing it directly from a balloon.