# for use in npm scripts
npm install electron-packager --save-dev

# for use from cli
npm install electron-packager -g

electron-packager C:/my-app MyApp

var packager = require('electron-packager');

packager({
    dir: '/',
}, function(err, path){
    if(err) throw err;
    // Application has been packaged
});

A convenient way to package your application is to write the scripts in your packages.json file and run them with the npm run command

{
    "name": "AppName",
    "productName": "AppName",
    "version": "0.1.1",
    "main": "main.js",
    "devDependencies": {
        "electron": "^1.6.6",
        "electron-packager": "^8.7.0"
    },
    "scripts": {
        "package-mac": "electron-packager . --overwrite --platform=darwin --arch=x64 --icon=images/icon.png --prune=true --out=release-builds",
        "package-win": "electron-packager . --overwrite --platform=win32 --arch=ia32 --icon=images/icon.png --prune=true --out=release-builds",
        "package-linux" : "electron-packager . --overwrite --platform=linux --arch=x64 --icon=images/icon.png --prune=true --out=release-builds"
    }
}

And to run them you just write:

npm run package-mac
npm run package-win
npm run package-linux

A breakdown of the command flags is:

electron-packager .     // this runs the packager in the current folder
--overwrite             // overwrite any previous build
--platform=darwin       // platform for which the binaries should be created
--arch=x64              // the OS architecture
--icon=images/icon.png  // the icon for the app executable
--prune=true            // this does not copy your dev-dependencies that appear in your packages.json
--out=release-builds    // the name of the folder were the binaries will be outputed

Before, running the scripts change the devDependencies to dependencies as electron-packager cannot bundle the packages in the devDependencies into the app. In packager.json, change the word (if it's there or if packages are installed using --save-dev in npm install) devDependencies to only dependencies.