What I've learned so far is that /// < reference >-ing a module with reference comments is not a good method.
For example: in case you have a file Foo and a file Bar. Both files use jquery, but only file Foo has a reference comment to jquery. If file Foo is deleted for some reason, your file Bar is broken, because the reference is missing.
If you are using TypeScript >= 2.0 It is better to define the TypeScript definition files (.d.ts) in your tsconfig.json under the "files" section.
This could look like this:
{
  "compileOnSave": true,
  "compilerOptions": {
    "noImplicitAny": true,
    "noEmitOnError": true,
    "removeComments": false,
    "sourceMap": true,
    "target": "es5", 
    "outDir": "./Scripts/"
  },
  "files": [
    "./src/foo.ts",
    "./src/bar.ts",
    "./Scripts/typings/jquery/jquery.d.ts",
    "./Scripts/typings/jqueryui/jqueryui.d.ts",
    "./Scripts/MicrosoftMaps/Microsoft.Maps.d.ts"
  ]
}
Using the /// directive (reference comments) is often used in examples to get you started quickly, but it is not a best practice. Also many examples come from a version < TypeScript 2.0.