Although it is always recommended to put JavaScript and CSS code into appropriate files (as .js and .css), most of major websites (like Amazon, facebook, etc.) put a significant part of their JavaScript and CSS code directly within the main HTML page.
Where is the best choice?
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).
Place your .js in multiple files, then package, minify and gzip that into one file.
Keep your HTML into multiple seperate files.
Place your .css in multiple files, then package, minify and gzip that into one file.
Then you simply send one css file and one js file to the client to be cached.
You do not inline them with your HTML.
If you inline them then any change to the css or html or js forces to user to download all three again.
The main reason major websites have js & cs in their files, is because major websites code rot. Major companies don't uphold standards and best practices, they just hack it until it works then say "why waste money on our website, it works doesn't it?".
Don't look at examples of live websites, because 99% of all examples on the internet show bad practices.
Also for the love of god, Separation of concerns please. You should never ever use inline javascript or inline css in html pages.
An interesting investigation might be whether they include various .css files regardless of the style blocks you're also seeing. Perhaps it's overhead or perhaps it's convenience.
I've found that while working with different styles of interface developer (and content deployers) that convenience/authority often wins in the face of deadlines and "getting the job done". In a project of a large scale there could be factors involved like "No, you ain't touching our stylesheets", or perhaps if there isn't a stylesheet using an http request already then convenience has won a battle against good practice.
If your css and javascript code is for a global usage, then it is best to put them into appropriate files. Otherwise, if the code is used just by a certain page, like the home page, put them directly into html is acceptable, and is good for maintenance.
Our team keeps it all seperate. All resources like this goes into a folder called _Content.
CSS goes into _Content/css/xxx.js
JS goes into _Content/js/lib/xxx.js (For all the library packages)
Custom page events and functions get called from the page, but are put into a main JS file in _Content/js/Main.js
Images will go into the same place under _Content/images/xxx.x
This is just how we lay it out as it keeps the HTML markup as it should be, for markup.
I think putting css and js into the main html makes the page loads fast.