In a React application, the distinction between .js and .jsx files is important for understanding how JavaScript (JS) and JavaScript XML (JSX) work together. Let's break this down:

1. JavaScript (.js)
Purpose: .js files are standard JavaScript files that contain plain JavaScript code. These files can be used anywhere in a project to define functions, classes, variables, and any other JavaScript constructs.
Content: A .js file can include functions, objects, and other constructs that handle the logic of your application. For example, you might define utility functions, data models, or service classes in .js files.
Usage in React: In a React application, .js files often contain non-JSX code, such as utility functions, configuration files, or components written without JSX. You can still write React components in .js files if you use the React.createElement function instead of JSX.
2. JavaScript XML (.jsx)
Purpose: .jsx files are designed specifically for writing React components that include JSX syntax. JSX is an XML-like syntax extension for JavaScript that allows you to write HTML elements in JavaScript code, which is then transformed into React elements.
Content: A .jsx file typically contains React components that include both JSX and JavaScript. The JSX syntax allows you to describe the UI structure directly within the JavaScript code, making the code more readable and closer to the final HTML output.
Usage in React: React components are often written in .jsx files because JSX makes it easier to visualize the component's structure. When a file includes JSX syntax, it's conventional to use the .jsx extension to indicate that the file contains JSX code, though this is not mandatory.
3. Differences and When to Use Which
Syntax Highlighting and IDE Support: Using .jsx for files with JSX code helps in better syntax highlighting and linting in many editors. Some IDEs and text editors have different rules for .js and .jsx files, providing enhanced support for JSX when the file is named with a .jsx extension.
Clarity: Naming your files with the appropriate extension helps developers understand what to expect from a file. If a file is named .jsx, it's immediately clear that it will contain JSX, making it easier for team members or collaborators to navigate the codebase.
Compatibility: While you can technically write JSX in .js files and the Babel transpiler will handle it, using .jsx is a best practice for clarity and maintainability. Modern React projects often use .js for plain JavaScript and .jsx for components containing JSX.
4. Transpilation
Babel: Whether you use .js or .jsx, JSX needs to be transpiled into standard JavaScript that browsers can understand. Babel is a popular tool for this task, transforming JSX into React.createElement calls.
Performance: There is no significant performance difference between using .js or .jsx because, after transpilation, both result in the same JavaScript code.

5. Historical Context
Early React: Initially, React components were written using React.createElement() without JSX. JSX was introduced later to simplify the creation of React elements by allowing developers to write HTML-like syntax directly in their JavaScript code.
Adoption of JSX: As JSX became more popular, developers started using .jsx to differentiate between plain JavaScript files and files containing JSX. Over time, it became a convention to use .jsx for files with JSX, even though modern build tools and transpilers like Babel can handle JSX in .js files as well.

6. Code Organization
File Naming Conventions: Consistent use of .js and .jsx can aid in organizing your codebase. For instance:
Components: Store React components in a components/ directory, using .jsx for components that use JSX.
Utilities: Store utility functions and helper modules in a utils/ directory, using .js since these files typically do not contain JSX.
Hooks: Custom React hooks can be stored in a hooks/ directory, usually using .js unless the hook returns JSX or involves rendering logic.
Index Files: You can create index.js files in directories to simplify imports. For example, an index.js in the components/ directory can export all components, allowing you to import them from a single source.