“Dark” essentially refers to the web servers that are connected to the Internet but are not publicly indexed. Some people further differentiate between the “deep” web and the “dark” web, where the dark part is intentionally anonymize via an intermediary service like proxying through a tor service, and the deep part is publicly viewable but just not indexed (either due to robots.txt permissions or just because it has yet to be indexed).
There’s also the “deep” and “dark” net, which refers to all unindexed Internet traffic, including non-www stuff like email, VoIP, FTP, SFTP, Gopher, BitTorrent, KaZaa, Hotline, and the myriad of other communication and information service technologies that run on top of the globally connected IP network.
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