How can I add a default header to my source files automatically in Eclipse?

If you want to add your comment a the top of the file (to add a copyright header), give a try to Eclipse Copyright Generator. There is a wizard that ask you what you want to include. Therefore you can add every kind of comment header.

After installation you get a new menu: Project > Apply Copyright....

In the include files field enter *.java to reduce the set of files.

see also this answer

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As indicated in the comments, there is an other tool provided by the Eclipse Fundation: Eclipse Copyright Tool (as part of their releng tools)

Comments generation is configured in:

Main Menu -> Window -> Preferences -> Java -> Code Style -> Code Templates -> Configure generated code and comments

You can change directly the New Java files template: Code -> New Java files -> Edit

As of Eclipse 3.6 version, it is already configured that for new Java files ${filecomment} is inserted, so it is probably better to edit it instead:

Comments -> Files -> Edit