With only the Java Developer Tools (JDT) installed the Project Explorer nearly looks and behaves for Java projects as the Package Explorer (including refactoring and other source code operations in the context menu). But project Explorer was usable for languages and project types as well.
Additional Plugins contributes "extra information" to the Project Explorer view making it much more "sophisticated". For example if you had the Web tools installed and you had a Dynamic Web project, the project Explorer shows you additio Nal tree nodes like Deployment descriptor and JavaScript Resources. You can see (and configure) all available contributions in Project explorer/customize View .../Content.
For example using SpringSource Tool Suite 2.1.0 I has additional nodes for Web projects, spring beans and Web services. Because of this I favor using the Project Explorer.
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What is the difference between Project Explorer and package Explorer in Eclipse