I\'m looking for a simple clock synchronization protocol that would be easy to implement with small footprint and that would work also in the absence of internet connection,
I was able to implement a parred down version of the Precision Time Protocol very quickly and easily based solely on the wikipedia article. If all you are interested in is synchronizing them with each other as opposed to synchronizing them with the outside world, you should be able to get millisecond accuracy with minimal effort.
The fundamental basics of the protocol involve the following:
If you need better stability, you can implement a phase locked loop or a linear regression or something similar to better control your jitter and avoid large swings due to network lags. There are a number of more complicated features specified by the protocol, but if you want to implement them depends on how close 'good enough' is.