There was/is a lot of confusion, as JSR-330 (Dependency Injection for Java) led by Rod Johnson (SpringSource) and Bob Lee (Google Inc.) became a part of Java EE 6. JSR-330 is very simplistic. It comes with own few annotations from the package: javax.inject. The package contains the following elements: Inject, Qualifier, Scope, Singleton, Named and Provider. Its the definition of the basic dependency injection semantics.
JSR-299 (Java Contexts and Dependency Injection), with Gavin King as lead, uses JSR-330 as base and enhances it significantly with modularization, cross cutting aspects (decorators, interceptors), custom scopes, or type safe injection capabilities. JSR-299 is layered on top of JSR-330.
It is amusing to see that the built-in qualifier @Named is not recommended and should be used only for integration with legacy code:
"The use of @Named as an injection point qualifier is not recommended, except in the case of integration with legacy code that uses string-based names to identify beans."
[3.11 The qualifier @Named at injection points, JSR-299 Spec, Page 32]
The relation between JSR-299 and JSR-330 is comparable to the relation between JPA and JDBC. JPA uses internally JDBC, but you can still use JDBC without JPA. In Java EE 6 you can just use JSR-330 for basic stuff, and enhance it on demand with JSR-299. There is almost no overlap in the practice. You can even mix JSR-299 / JSR-330 with EJB 3.1 - to streamline your application.