You seem pretty confused.
Web Servers are written in C/C++ normally because they need to provide high performance but you can write one in any programming language, but I don't think your asking about this.
.NET is just a term which encapsulates a range of technologies from MS (Framework).
The most popular server side scripting languages would probably be PHP, ASP(.NET) at the moment. Though there are plenty of others.
Java is mainly used for application development now (java applets still exist but are a past technology imo). You might be mistaking it for Javascript which is a totally different language and is used heavily in web dev.
