Anant Shrivastava has posted a whitepaper providing a rundown of application fingerprinting methodologies, as well as comparisons of various tools such as W3af, BlindElephant, and Wapplyzer.

"This Paper discusses about a relatively nascent field of Web Application
finger printing, how automated web application fingerprinting is performed
in the current scenarios, what are the visible shortcomings in the approach
and then discussing about ways and means to avoid Web Application Finger
Printing."

Link: http://anantshri.info/articles/web_app_finger_printing.html