There are three big problems with global variables:
- name collisions
- code complexity
- garbage collection
Name collision
The problem with having variables in global scope is that you have less control over what else is in that scope. Your code uses a ga_ variable globally and works fine, but when you add a Google Analytics snippet that uses the same variable things unexpectedly fail and it can be quite hard to see why your shopping cart fails 2 out of 3 page loads.
If you can wrap your code in an IIFE to prevent having any variables in global scope, you should do that. Obviously there are cases where you actually want to have your code accessible globally (ex: jQuery library). In those cases, it is best practice to keep all your stuff in a single namespace (jQuery) with a relevant name.
Code complexity
It is usually a good idea to partition your code so that individual pieces have minimal interactions with each other. The more pieces interact the harder it is to make changes and to track down where bugs come from. Obviously a global variable can be accessed anywhere so when you have a problem with some code that accesses a global variable, you have to inspect every usage of that variable which can be quite a big pain. The thing to do to avoid these pains is to keep variables as local as they can be and encapsulate pieces of code so they can't interact with each other except through specific interfaces.
Memory leaks
In JavaScript you have little control over the garbage collection process. All that is guaranteed is that if you can access a variable it will not be garbage collected. This means that if you want something to be garbage collected, then you must make sure you can't access it anymore. While a global i variable which keeps a number won't be a big deal, as @Boluc Papuaccoglu mentioned when your global variable keeps more and more properties over time (an array of XHR requests for example, or array of created DOM objects), the memory consumption turn into a big deal.
All of these situations are worst case scenarios and you probably won't have issues with a small application. These recomendations have most value when you're starting to learn programming because they develop good habits and when you're working on complex applications when they save you time and money wasted on debug or difficult to do improvements.
