As part of a new project EFF "Test Your ISP" Project | Electronic Frontier Foundation the EFF recently posted a detailed procedure for testing if an ISP is interfering with connections and transfers. It was used to show Comcast was interfering with gnutella.

Detecting packet injection: a guide to observing packet spoofing by ISPs | Electronic Frontier Foundation

The test requires two people, with a fairly high level of expertise, and has been used to hold ISPs legally accountable.

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