Can a helicopter like the R44 be lifted up by his rotor head? I am curious if a rotorcraft could be suspended from rotorhead for an extended period of time.  

I am curious about R22 and R44.  I believe I have seen them in the shop lifted up from the 2 holes in the rotor head.  

I am also curious if all helicopters have mount/lift points in the rotor head like an MD500C. Would you be able to do the same? 

Or are you better lifting from the skids for a longer term lifting?
Yes, but you better know what the heck you are doing. :) Whether an individual helicopter can be lifted this way is a different question. You'd have to look at the maintenance manual for the individual aircraft for the answer.