Dr. Richard Carrier - a historian with a expertise in ancient science as well as the historical Jesus - has applied Bayes' theorem to his work with the historical method. Off the top of my head, I know he's used Bayesian reasoning in the articles he contributed to the books The Christian Delusion and The End of Christianity. (In the end notes, he explicitly puts his arguments in terms of Bayesian probability theory.) If memory serves, he's also authoring a book which explains Bayes' theorem and its application to the historical method.

Coincidentally, it's through his work that Iearned about Bayes' theorem and I first learned about Dr. Carrier through lukeprog's podcast "Conversations from the Pale Blue Dot."

Edit: The podcast is located here http://commonsenseatheism.com/?p=10150 . I highly recommend it, as he discusses his application of Bayes' theorem to the historical method and its superiority to abductive reasoning.