There is no absolute tool to write a program with in .NET; as in Java you have several at your disposal to do what you want. You can go the "Microsoft way" using only Microsoft technologies all the way or you can use third party tools for nearly everything. Let's take the example of DBMS access:
- Using Microsoft tools
- ADO.NET ("standard" access to a DBMS)
- Linq to SQL (ORM)
- EntityFramework (ORM, similar to Hibernate)
- Using third-party tools
For every "part" of an application you have that choice, be it logging frameworks, testing frameworks, IOC frameworks, etc. In the beginnings of .NET there was only the "Microsoft Way" due to lacking third-party tools, now you have the choice.
To answer your other question on .NET web development, companies may use:
- "old school" ASP.NET WebForms
- ASP.NET MVC3
- Silverlight (as a separate application, or in combination with ASP.NET applications)
As of now, ASP.NET MVC seems to be the preferred choice, see #1, #2 or #3 (this one to indicate that ASP.NET WebForms has its advantages)
One thing that @Anand is right about: if you know Java, use C#.