What program do you use to program using C++ or website design or anything!
I'd tend to disagree on starting out using the command-line tools maybe for your first project to get a sense of it. Its the way I started but only because there was no other way to do it. The IDE tool provides an organization to your projects and the method lookup feature when you type . after an object is priceless. For school work, we would create a project for the class homework and separate packages for each assignment.
An IDE like NetBeans also provides line by line debugging that is far superior to the command line debugger although beginners tend to use the poor man's debugger the lowly print statement.
The best command line editor to use is vim as it runs everywhere on all platforms Windows, Linux... But best editor suggestions create religious wars. THink of VIM like American Express its everywhere you want to be. :-)
For Java the BlueJ IDE is is often used for introductory courses. Its a simple IDE with many cool features. For heavier work then NetBeans or Eclipse. I used to use Eclipse for everything getting the third party plugins for it but then discovered that NetBeans had most of the plugins I used already installed in the distribution and so I switched.