Which one of the 3 yields is commonly used in calculations such as the benchmark for the risk free rate?
Classically, it used to be par yield. However, given the current state of affairs, it's not even clear that using treasuries is the correct approach.
Here's a good summary: http://www.pimco.co.uk/EN/Insights/Pages/Finding-Sea-Level-for-Interest-Rates.aspx