You're right. Far too many sites depend on Javascript and Flash to function. In my opinion, sites that can't function without those are broken.
With javascript it's not a document, it's an application.
If you are writing an app, then sure, use javascript, and don't worry about it (even if you could do it server side, I rarely see the point).
But if you are writing a document then you should at least have a fallback, and reserve javascript for less important "flair".