FOR TYPESCRIPT 1.7+

It looks like standard is changing again, where the below 0.9+ method still works, but with ES6 coming the following module loading could be used. (reference: https://github.com/TypeStrong/atom-typescript/issues/237#issuecomment-90372105)

import * as $ from "jquery";

and even partial ones

import {extend} from "jquery"; 

(this still require the jquery.d.ts, if tsd is installed – tsd install jquery)

to install tsd: npm install tsd -g

FOR TYPESCRIPT 0.9+

/// <reference path="../../typings/jquery/jquery.d.ts" />
import $ = require('jquery');

//Do your stuff

And also, if your jquery.d.ts do not define a external module, add the following to jquery.d.ts:

declare module "jquery" {
    export = $;
}