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Namespacing and building sites using JavaScript classes (as opposed to just a bunch of global functions) can definitely help with this. There are various ways around the issue of onload conflicts: it's possible to register multiple event handlers for a single event, like onload or onbeforeunload; global code can sometimes be used to achieve a similar effect (or to register event handlers); and the order of script and css loading (the order they are specified in the source) can be used to some extent to affect how things execute.
But, of course, one needs to design one's pages and site around what's going to be on them. This is no less true when using Flash than when using JavaScript. Just randomly plunking content into a page is always a recipe for disaster. So, even if many of today's sites are built around the fact that they are serving ads with Flash, companies redesign sites all the time, and competent developers will be able to deal with the issues involved, whether they be Flash or JavaScript related.
So, this is not a "JavaScript issue", it's a general issue of all web development.







