module.js this error talks about is?just found it here
load function thinks the command was a '.js' file. How can i add extension handlers for '.cmd' files????
After creating a project using yo and generator-gulpplugin-coffee, I have run into an issue straight away with the command npm test
The full command listed in the base package.json "test" paramater is 
coffeelint gulpfile.coffee index.coffee test -f ./coffeelint.json && istanbul test _mocha --report lcovonly -- ./test/*.coffee --require coffee-script/register --reporter spec
The coffeelint works fine when i extract that command and run it, however the istanbul test _mocha... fails with an Unexpected token ILLEGAL error at the '@' symbol in the _mocha.cmd file:
$ npm test
> [email protected] test C:\Users\me\code\something
> coffeelint gulpfile.coffee index.coffee test -f ./coffeelint.json && istanbul test _mocha --report lcovonly -- ./test/*.coffee --require coffee-script/register --reporter spec
  ✓ gulpfile.coffee
  ✓ index.coffee
  ✓ test/main.coffee
✓ Ok! » 0 errors and 0 warnings in 3 files
C:\Users\me\code\something\node_modules\.bin\_mocha.CMD:1
(function (exports, require, module, __filename, __dirname) { @IF EXIST "%~dp0
                                                              ^
SyntaxError: Unexpected token ILLEGAL
    at exports.runInThisContext (vm.js:73:16)
    at Module._compile (module.js:443:25)
    at Object.Module._extensions..js (module.js:478:10)
    at Module.load (module.js:355:32)
    at Function.Module._load (module.js:310:12)
    at Function.Module.runMain (module.js:501:10)
    at runFn (C:\Users\me\code\something\node_modules\istanbul\lib\command\common\run-with-cover.js:122:16)
    at Object.run (C:\Users\me\code\something\node_modules\istanbul\lib\command\common\run-with-cover.js:254:9)
    at TestCommand.Command.mix.run (C:\Users\me\code\something\node_modules\istanbul\lib\command\test.js:27:22)
    at runCommand (C:\Users\me\code\something\node_modules\istanbul\lib\cli.js:78:19)
I've tried updating the libraries without success, here is my package.json:
{
  "name": "dadeda",
  "version": "0.0.0",
  "description": "A plugin for gulp",
  "keywords": [
    "gulpplugin"
  ],
  "repository": "me/dadeda",
  "author": {
    "name": "me",
    "email": "[email protected]",
    "url": "http://methere.com"
  },
  "files": [
    "index.js"
  ],
  "scripts": {
    "prepublish": "gulp coffee --require coffee-script/register",
    "test": "coffeelint gulpfile.coffee index.coffee test -f ./coffeelint.json && istanbul test _mocha --report lcovonly -- ./test/*.coffee --require coffee-script/register --reporter spec",
    "coveralls": "cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js"
  },
  "dependencies": {
    "gulp-util": "^3.0.0",
    "through2": "^0.6.1"
  },
  "devDependencies": {
    "coffee-script": "^1.7.1",
    "coffeelint": "^1.4.0",
    "coveralls": "^2.8.0",
    "del": "^1.2.1",
    "gulp": "^3.5.2",
    "gulp-coffee": "^2.1.2",
    "istanbul": "^0.3.19",
    "mocha": "^2.2.5",
    "should": "^7.1.0"
  },
  "engines": {
    "node": ">=0.10.0",
    "npm": ">=1.3.7"
  },
  "license": "MIT"
}
I am using windows 10, node 0.12.7, npm 2.11.3.
This is an issue on Windows machines as it can't execute the _mocha file as javascript - as you have identified.
The workaround is to pass the full path of the mocha file (as described in this issue):
istanbul test node_modules/mocha/bin/_mocha
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