For any sort of web development, I would recommend apache2. For databases, I would recommend mysql-server or postgresql. For Java (as well as C++ and some others), a popular option is eclipse, although netbeans is also good.
If you want to see what’s going on under the hood, wireshark is a great network monitoring utility that shows you every detail of all network traffic for the server.
solved What are the essential things that a new ubuntu server should have installed, for development purposes? [closed]