Obviously the worst thing about proprietary JavaScript is that it's proprietary. You don't have the 4 freedoms.

Besides that JavaScript can be used for snooping various things, some listed at https://panopticlick.eff.org/

Also, the JavaScript sandboxes on many applications are not too good and there are quite a few exploits that take advantage of JS. E.g. https://www.mozilla.org/en-US/security/known-vulnerabilities/firefox/

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