There was a thread started awhile back (on full disclosure) and I just figured I'd summarize the apps that they put out there for fingerprinting web sites:
http://sucuri.net/?page=docs&title=fingerprinting-web-apps
There is also a live tool for you to test with any site:
http://sucuri.net/?page=docs&title=fingerprinting-web-apps#v6
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http://www.morningstarsecurity.com/research/whatweb
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http://www.mytty.org/wafp/
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I haven't checked any of them out, but wanted to add them here so I could find them if/when I'm looking in the future! If you have any others feel free to add them in a reply to this post.
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