If you have a favorite tool or a good story on how you chose a programming language, please leave a comment!
1. What programming language should I learn?
This is like asking a stranger who you should marry. You can write great web applications in PHP... or ASP.NET... or node.js... and so on. So how do you choose? PHP makes me want to pour bitter coffee in my eyes, so I'll never learn it. Easy choice.
At first, just focus on the basics
That is what the server-side languages will deliver to the client, so you should have a good understanding of them before you dive into the server-side coding itself.
The only guidance on server-side languages I would give is this: experiment and simply go with what you like. Try some tutorials like NodeSchool or ASP.NET MVC. Stay away from WebForms. WebForms should be banished to the dark underbelly of the interwebs where it can hang out with the Space Jam website.
2. What IDE should I use?
This may be determined by what language you end up using, and it is also a matter of preference. For your own educational experience, don't use a WYSIWYG program (if web technologies were hand tools, WYSIWYGs would be a plunger. see why). If you want to drag stuff around and call yourself a web developer, you might as well just make the website in Microsoft Word and "Save as Web Page".
But what is the best IDE???
I don't know. Where can I get the best coffee in New York?
Github at its core is version control software. Version control is a system that allows you to easily manage your code (and subsequent changes to your code). Need more explanation? Watch a quick 6 minute video explaining version control. No, I didn't watch it. But judging by the guy on the cover, it's going to be very informative and answer all of your questions.
Aside from version control, GitHub is an invaluable code resource for you, allowing you to easily download other peoples' code so you can experiment for yourself. Start using it.
4. Stack Overflow
Stack Overflow is "a question and answer site for professional and enthusiast programmers". It can be a great resource for quick answers to your problems. Aside from the answers, I like it as a place where you can learn by helping others.
Be sure to read How to Ask and How to Answer thoroughly or your questions may get flamed out of existence, leaving you bitter and penning blogs like Why Stack Overflow Sucks... and as a programmer, neither you or your coffee should be bitter.
JSFiddle is an online playground for you to experiment with code. The site is good for learning and is also helpful to share code snippets with others if you are having trouble. They can edit, fix, and share the code back to you. Need more explanation? Go through a JSFiddle Tutorial. No, I didn't read it. But judging by the color scheme and lack of Comic Sans font, I think it will be very informative and answer all of your questions.