Netbeans and Eclipse are editors/IDEs. They are simply tools that allow you to write code & interface with the rest of your toolset. It's like the difference between writing a novel on a legal pad or a Moleskine notebook - the words are all the same but it feels a little different when you put them on the page.

Java and C++ are languages. They are different ways of expressing ideas to computers. They have different syntax, semantics and standard libraries. This would be like writing your novel in French or English - you can tell the same story but the way you express it might be a little different.

The run-time environment is where the program actually works. This includes your compiler, libraries and possibly a virtual machine. The difference here would be like writing your novel as a commedy or a serious drama - you're telling the same story but the way you tell it is completely different.

It is important to note that a programming language, in the abstract, is completely separate from the concrete implementation of the language. A good example would be Python - you have the standard implementation (Cpython) which has one set of libraries and runs in its own VM and Jython, a completely different implentation of the language specification that runs inside the Java Virtual machine and uses the Java libraries. Similarly, if you're working with Visual studio, you can chose to take your C++ code and compile it to either native code or target the CLI (.NET virtual machine).

What is a virtual machine? It's basically a program that runs programs. If you have ever played a video game in an emulator (or even a Flash game), you've used a virtual machine. The difference is that something like the Java JVM or the .NET CLI pretends to be a new machine that doesn't physically exist rather than recreating something concrete.

There are many reasons why somebody would create a VM. One big reason is that it's possible to completely isolate a program from the rest of the system if it's in a VM - sandboxing was one of the big selling points of Flash and Java (as a browser plug-in). Another is that your program will run on any machine be it a Mac, Windows PC or Linux - a great example of this is how the Z Machine that Infocom used for their games in the 80s allowed them to write & compile their games a single time and run them on every computer of the era, be it Apple, Atari, Commodore, PC or any of the other dozen or so different machines that were in use at the time.

As for your final question, the Oracle/Google fiasco has three major points. The first was a patent about how somebody would implement a VM; they lost this point. The second was claiming that an API (specifically the Java Standard Library) was a copyrighted work; they lost on this point. The third was that Google stole code from them; in the millions of lines that make up a Java system, they found 9 - they have not decided on this but the Judge, a novice programmer, had said that "any schoolboy could write this in an hour" and it shouldn't be considered relevant.