It was a big problem in the JavaScript world, until JQuery and YUI and Google came out and said "Thou shalt not modify Object.prototype" and started leading by example. But Prototype and Mootools and a bunch of smaller libraries still modify the prototypes of built-in objects, which is the main reason I won't go near those libraries. Unfortunate, since they're otherwise pretty good...

I think new versions of JSON.js (json2.js) don't modify Object.prototype anymore - Crockford has certainly learned his lesson.