Sample JavaScript file added with ScriptTag resource. This sample file is meant to teach best practices. Your app will load jQuery if it's not defined. Your app will load jQuery if jQuery is defined but is too old, e.g. < 1.7.

gistfile1.js

/* Sample JavaScript file added with ScriptTag resource. 
This sample file is meant to teach best practices.
Your app will load jQuery if it's not defined. 
Your app will load jQuery if jQuery is defined but is too old, e.g. < 1.7. 
Your app does not change the definition of $ or jQuery outside the app. 
Example: if a Shopify theme uses jQuery 1.4.2, both of these statements run in the console will still return '1.4.2'
once the app is installed, even if the app uses jQuery 1.9.1:
jQuery.fn.jquery => "1.4.2" 
$.fn.jquery -> "1.4.2"
*/

/* Using a self-executing anonymous function - (function(){})(); - so that all variables and functions defined within 
aren’t available to the outside world. */

(function(){
  
/* Load Script function we may need to load jQuery from the Google's CDN */
/* That code is world-reknown. */
/* One source: http://snipplr.com/view/18756/loadscript/ */

var loadScript = function(url, callback){
 
  var script = document.createElement("script");
  script.type = "text/javascript";

  // If the browser is Internet Explorer.
  if (script.readyState){ 
    script.onreadystatechange = function(){
      if (script.readyState == "loaded" || script.readyState == "complete"){
        script.onreadystatechange = null;
        callback();
      }
    };
  // For any other browser.
  } else {
    script.onload = function(){
      callback();
    };
  }

  script.src = url;
  document.getElementsByTagName("head")[0].appendChild(script);
    
};

/* This is my app's JavaScript */
var myAppJavaScript = function($){
  // $ in this scope references the jQuery object we'll use.
  // Don't use jQuery, or jQuery191, use the dollar sign.
  // Do this and do that, using $.
  $('body').append('<p>Your app is using jQuery version '+$.fn.jquery+'</p>');
};

/* If jQuery has not yet been loaded or if it has but it's too old for our needs,
we will load jQuery from the Google CDN, and when it's fully loaded, we will run
our app's JavaScript. Set your own limits here, the sample's code below uses 1.7
as the minimum version we are ready to use, and if the jQuery is older, we load 1.9. */
if ((typeof jQuery === 'undefined') || (parseFloat(jQuery.fn.jquery) < 1.7)) {
  loadScript('//ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js', function(){
    jQuery191 = jQuery.noConflict(true);
    myAppJavaScript(jQuery191);
  });
} else {
  myAppJavaScript(jQuery);
}

})();

When jQuery version '1.10' or higher is already loaded, parseFloat(jQuery.fn.jquery) will return 1.1, causing another jQuery file to be downloaded unnecessarily.

jQuery.fn.jquery = '1.7.1'; parseFloat(jQuery.fn.jquery) === 1.7;
// higher version returns a lower float
jQuery.fn.jquery = '1.10'; parseFloat(jQuery.fn.jquery) === 1.1;

Workaround (line 58) with minimum version 1.7.1:

if ((typeof jQuery === 'undefined') || (parseInt(jQuery.fn.jquery) === 1 && parseFloat(jQuery.fn.jquery.replace(/^1\./,'')) < 7.1)) {

Forked gist with workaround (updated Apr 7, 2015):
https://gist.github.com/lulessa/a0f112dcb816bf1ccbd6

How do I also load jQuery UI into this script?

@jordanblink
Not sure if you are still looking but this forked code might work for you:
https://gist.github.com/Modules4U/01de3d24b487583041e9ed7eb422e366

I'm seeing apps load jquery in my theme even though the jQuery version is higher than the version checked and 1.11 instead of 1.7 and the apps are all loading jquery anway (five times on one page...)

What is the fix for fixing my store vs fixing the app code because that is beyond the scope of what I can do? Is my only choice to remove the apps?

Hello! Very appreciate your sample, but can I ask where do i put these code?
I'm developing a Shopify Public Web App and I need show a Grid View on User Page to show some data on my server when they was login. But I don't really know where to write javascript for my app. I was success on create app and installed it. I read document say should use ScriptTag and don't touch liquid template.

Hello! Very appreciate your sample, but can I ask where do i put these code?
I'm developing a Shopify Public Web App . But I don't really know where to write javascript for my app. I was success on create app and installed it. I read document say should use ScriptTag and don't touch liquid template.

still works like a charm, thanks :)

If theme is using SLIM version of jQuery then above code snippet would load that and if your code is dependent on some ajax calls which SLIM version doesn't support, your app would fail. I got around this by adding one more check for jQuery.fn.jquery.includes("-ajax").

Let me know if there is other way of handling this.