Where Should I Put the CSS and JavaScript Code in an HTML Webpage

Where should I put the CSS and Javascript code in an HTML webpage?

In my opinion the best practice is to place the CSS file in the header

<head>
  <link rel="stylesheet" href="css/layout.css" type="text/css">
</head>

and the Javascript file before the closing </body> tag

  <script type="text/javascript" src="script.js"></script>
</body>

Also if you have, like you said two CSS files. The browser would use both. If there were any selectors, ie. .content {} that were the same in both CSS files the browser would overwrite the similar properties of the first one with the second one's properties. If that makes sense.

Where to place JavaScript in an HTML file?

The Yahoo! Exceptional Performance team recommend placing scripts at the bottom of your page because of the way browsers download components.

Of course Levi's comment "just before you need it and no sooner" is really the correct answer, i.e. "it depends".

Put CSS and JavaScript in files or main HTML?

http://developer.yahoo.com/performance/rules.html#external

Yahoo (even though they have many inline styles and scripts), recommends making them external. I believe google page speed used to (or still does?) do the same as well.

It's really a logical thing to have them separate. There are so many benefits to keeping CSS and JS separate to the HTML. Things like logical code management, caching of those pages, lower page size (would you rather a ~200ms request for a 400kb cached resource, or a 4000ms delay from having to download that data on every page?), SEO options (less crap for google to look through when scripts/styles are external), easier to minify external scripts (online tools etc), can load them synchronously from different servers....

That should be your primary objective in any website. All styles that make up your whole website should be in the one file (or files for each page, then merged and minified when updated), the same for javascript.

In the real world (not doing a project for yourself, doing one for a client or stakeholder that wants results), the only time where it doesn't make sense to load in another javascript resource or another stylesheet (and thus use inline styles/javascript) is if there's some kind of dynamic information that is on a kind of per-user, per-session or per-time-period that can't be accomplished as simply any other way. Example: when my website has a promotion, we dump a script tag with a small JSON object of information. Because we don't minify and merge multiple files, it makes more sense to just include it in the page. Sure there are other ways to do this, but it costs $20 to do that, whereas it could cost > $100 to do it another way.

Perhaps Amazon/Facebook/Google etc use so much inline code is so their servers aren't taxed so much. I'm not too sure on the benchmarking between requesting a 1MB file in one hit or requesting 10 100KB files (presuming 1MB/10 = 100KB for examples' sake), but what would be faster? Potentially the 1MB file, BUT smaller requests can be loaded synchronously, meaning each one of those 10 requests could come from a separate server/domain potentially, thus reducing overall load time.

Further, google homepages for example seem to dump a JSON array of information for the widgets, presumably because it compiles all that information from various sources, minifies it, caches it, then puts in on the page, then the javascript functions build the layout (client side processing power rather than server-side).

Where should I put script tags in HTML markup?

Here's what happens when a browser loads a website with a <script> tag on it:

Fetch the HTML page (e.g. index.html)
Begin parsing the HTML
The parser encounters a <script> tag referencing an external script file.
The browser requests the script file. Meanwhile, the parser blocks and stops parsing the other HTML on your page.
After some time the script is downloaded and subsequently executed.
The parser continues parsing the rest of the HTML document.

Step #4 causes a bad user experience. Your website basically stops loading until you've downloaded all scripts. If there's one thing that users hate it's waiting for a website to load.

Why does this even happen?

Any script can insert its own HTML via document.write() or other DOM manipulations. This implies that the parser has to wait until the script has been downloaded and executed before it can safely parse the rest of the document. After all, the script could have inserted its own HTML in the document.

However, most JavaScript developers no longer manipulate the DOM while the document is loading. Instead, they wait until the document has been loaded before modifying it. For example:

<!-- index.html -->
<html>
    <head>
        <title>My Page</title>
        <script src="my-script.js"></script>
    </head>
    <body>
        <div id="user-greeting">Welcome back, user</div>
    </body>
</html>

JavaScript:

// my-script.js
document.addEventListener("DOMContentLoaded", function() {
    // this function runs when the DOM is ready, i.e. when the document has been parsed
    document.getElementById("user-greeting").textContent = "Welcome back, Bart";
});

Because your browser does not know my-script.js isn't going to modify the document until it has been downloaded and executed, the parser stops parsing.

Antiquated recommendation

The old approach to solving this problem was to put <script> tags at the bottom of your <body>, because this ensures the parser isn't blocked until the very end.

This approach has its own problem: the browser cannot start downloading the scripts until the entire document is parsed. For larger websites with large scripts and stylesheets, being able to download the script as soon as possible is very important for performance. If your website doesn't load within 2 seconds, people will go to another website.

In an optimal solution, the browser would start downloading your scripts as soon as possible, while at the same time parsing the rest of your document.

The modern approach

Today, browsers support the async and defer attributes on scripts. These attributes tell the browser it's safe to continue parsing while the scripts are being downloaded.

async

<script src="path/to/script1.js" async></script>
<script src="path/to/script2.js" async></script>

Scripts with the async attribute are executed asynchronously. This means the script is executed as soon as it's downloaded, without blocking the browser in the meantime.
This implies that it's possible that script 2 is downloaded and executed before script 1.

According to http://caniuse.com/#feat=script-async, 97.78% of all browsers support this.

defer

<script src="path/to/script1.js" defer></script>
<script src="path/to/script2.js" defer></script>

Scripts with the defer attribute are executed in order (i.e. first script 1, then script 2). This also does not block the browser.

Unlike async scripts, defer scripts are only executed after the entire document has been loaded.

According to http://caniuse.com/#feat=script-defer, 97.79% of all browsers support this. 98.06% support it at least partially.

An important note on browser compatibility: in some circumstances, Internet Explorer 9 and earlier may execute deferred scripts out of order. If you need to support those browsers, please read this first!

(To learn more and see some really helpful visual representations of the differences between async, defer and normal scripts check the first two links at the references section of this answer)

Conclusion

The current state-of-the-art is to put scripts in the <head> tag and use the async or defer attributes. This allows your scripts to be downloaded ASAP without blocking your browser.

The good thing is that your website should still load correctly on the 2% of browsers that do not support these attributes while speeding up the other 98%.

References

async vs defer attributes
Efficiently load JavaScript with defer and async
Remove Render-Blocking JavaScript
Async, Defer, Modules: A Visual Cheatsheet

Why is the standard to put the css and js file at the top and bottom of the page (respectively)?

That's not entirely correct. Said simply:

Style declarations should be as close to the top as possible, since browsers won't render your page before loading the CSS (to avoid a flash of unstyled content)
Script tags should be as close to the bottom as possible, since they block browsers from parsing after the tag before it is loaded and complete (because the script may change the document with document.write)

If you're interested in frontend performance, I highly recommend reading High Performance Web Sites: Essential Knowledge for Front-End Engineers by Steve Souders.

Where Should I Put the CSS and JavaScript Code in an HTML Webpage