ECHELON is a conspiracy theory suggesting that there is a system of international data collection and analysis being conducted on all private electronic communication. The project is very similar to the USA PATRIOT ACT, and appropriately, is believed to be headed by the US, accompanied by several other mostly NATO nations. The speculated purpose of the system is not only collect worldwide electronic communication signal information, but also check them for content (refer back to USA PATRIOT ACT, where the content in question was terrorist intent).
The recent (mid to late 2013) NSA and government leaks have lead to suggestions that said leaks confirm the reality of this project, albeit under a different term: codenamed "PRISM", again suggested to be headed by the US.
The use of ECHELON in the story is only mentioned in the VN, since in the anime only the "main" storyline exists, and in a less detailed form.
In the VN, the method of transcending the 1.0% divergence is not simply to undo all of the D-mails, but rather to undo the fact that SERN ever notices the first D-mail, which requires Okabe to undo all (not mentioning side routes) the past D-mails to get the IBM 5100 back.
SERN notices the original D-mail through usage of the ECHELON system, which was checking for time-machine related content (or possibly Makise Kurisu related content, since the original D-mail contained nothing time or time machine related except for the future send date). The text content of this D-mail that was recorded by ECHELON was stored inside SERN's hidden IBN 5100 database, and had to be deleted in order to cross the 1.0% divergence.