It is widely recommended that JS files should be put at the bottom of page to allow html codes to be loaded first. In this case, visitors will see something when waiting for
Edit: I am adding another point in response to the cotton I'm seeing in peoples ears on this topic.
Additional point #5. If you are seriously concerned about handling behavior on JS-fail and by that I mean, people browsing with JS turned off, what you should be doing is embracing the notion of progressive enhancement. For instance, you could design an accordion menu to act as a flyout-menu on-hover by default, yes with CSS only, and then remove that behavior by changing key classes when JS is enabled. That way users have access to the links without JS if they should turn it off but they get the enhanced behavior when JS is working.
But what you should not be trying to handle is the absence of entire JS files on pages that are supposed to have them because the page was mangled on the back-end. Handling the unexpected is one thing, but handling the failure to finish building an HTML file before it's served should not ever be considered an acceptable scenario in production, especially if you have actual back end code in your templating language (which you shouldn't) waiting to spill out and give would-be hackers something potentially interesting to look at. Broken pages should be served as error messages.
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Dead wrong. Any time you use JS to tweak the initial static look of your page, you're doing it wrong. Maintain that separation of concerns and your pages will be much more flexible. Using JS to tweak the STATIC styles of your pages isn't modern, it's bass-ackwards and you can tell the jQuery mobile guys I said as much. If you absolutely must support IE6 and IE7 and IE8 tell your client how much it's going to cost them to cut out rounded gradient corners all over the place if they refuse to accept anything as an alternative to absolute graceful degradation for 5% of their client-base.
If your pages, with no JS beforehand are taking that long to load, you have other problems that need to be addressed. How many resources are you loading? What ungodly pre-processing is your PHP up to? I call back end or design shenanigans.
Are you saying it's half-acceptable to have half a page with working JS rather than completely unacceptable? Don't let go of that client, whoever they are.
jQuery, when minimized is about the size of a medium-sized JPEG.
Note: It is not entirely unacceptable to have some JS up top. Some specialized code like analytics stuff or canvas normalizers require it. But anything that doesn't need to be should be at the bottom. Every time JS is parsed, the entire page load and flow calculation process stalls out. Pushing your JS to the bottom improves perceived page load times and should also serve to provide evidence that somebody on your team needing a swift kick in the butt to figure out why their code is tanking or what could be done with their 25 megabyte png-24s that they just shrunk down rather than reformatted.