This volume (33) of Hesperia Supplements includes an excellent article by D. J. Ian Begg reviewing the present study and understanding of the context and interpretation of Minoan "mason's marks". For anyone who is curious about the marks incised in stone at Knossos, Phaistos, Hagia Triada, Gournia, etc., this article is a fantastic place to start.
One of my favourite quotes from this paper is "It is a truism in archaeology that religious interpretations are often assigned to artifacts that are otherwise as yet inexplicable; mason's marks would appear to be particularly susceptible to such interpretations." Indeed! This has often been the case since as early as Sir Arthur Evans began interpreting the purpose of the labris marks in his "pillar crypts" at Knossos.
The article does an excellent job of reviewing religious and secular interpretations, and considers contemporary evidence from Egypt and Cyprus, as well as taking a look at the use of mason's marks in post-Minoan times on Crete and in Greece. One especially exciting observation in this article, courtesy of Oliver Pelon, is the reinterpretation of an incised stone altar at Malia. Both the altar and a supporting pillar in Silo 2 at Malia share a very interesting distinction: both are incised with a simple cross facing south and a star facing east.
Minoan mason marks @ Flickr