Calculate Phase angle between two signals i.e. digital Phase meter
A quick and dirty method is to compare the energy of the sum (L+R) to the energy of the difference (L-R). This gives a a crude single-number phase difference and is good at finding things like polarity flips etc.

As Dilip pointed out, the concept of phase difference between uncorrelated signals is meaningless. Even if they are correlated, the phase difference tends to be a function of frequency, so a single number isn't particularly helpful either. Most real world stereo audio signals are partially correlated, which complicates the matter further. In order to really answer the question, you need to properly define what you mean by phase difference and what you are planning to do with it.