I would recommend . . . I would start with this progression . . . HTML->CSS->Javascript then PHP/MySQL then once you have a handle on creating a simple web app with PHP/MySQL look at either Rails/Ruby or Laravel/PHP . . . it's tough to understand all the magic going on in Rails/Laravel till you've created a basic app from scratch Login/Logout/CRUD etc . . . Railscasts.com and Laracasts.com are great tools for learnin…
JavaScript lets you control HTML elements, so it would be rather hard to begin with just JavaScript. Styles in CSS are currently indispensable when writing any HTML unless you want to rely on crude default formatting. That's why it's HTML -> CSS -> JS and not the other way around.
Moreover you have to understand that JavaScript is a client-side scripting language, that is to say that your scripts will be downloaded and executed solely and entirely on your computer. You will not have any way to open, read and write to files (except for cookies), because your script "lives" only inside the browser.
If you want your code not to be seen by a visitor of your website, or if you want the code to be executed before the page is downloaded and displayed in a browser, you need a server-side scipts like PHP or ASP so that for example the visitor has only access to the parts of the website you want him/her to read, or display content depending on the user login and password.
Later you will see that for storing and manipulating larger amounts of data you'll need a data base server, which makes sorting and managing information much easier and faster than if you'd accessed files directly from your servers' hard drive.
PHP and MySQL are for free and therefore they are recommendable for beginners - alternatives are Microsoft's .Net + MS SQL and many many other, which are arguably more robust for commercial, enterprise level applications.
Node.js is however a more modern way of doing things on-line, PHP belongs to the 2000s.
jQuery is good once you realise why plain javascript s*cks a great deal ;)
Staring your journey with online tools such as JS is ok, but it may be difficult to later jump into more... how should I put it... "serious?" languages - once you want to build your own standalone application software that runs outside a browser (not only because you have to use a compiler, but also because you have to pay attention to more details and plan ahead). For instance it's not impossible, but it seems that, switching from strong typed languages like C to weak typed is easier than the other way around.
Please do never underestimate or neglect learning about design patterns, data structures and algorithms no matter what language you're using or intend to learn.