I have twelve squares and six of those are selected randomly and a style then applied. This is achieved by generating random values from an array of unique values. The problem
Just for the sake of simplicity I will assume your elements have a class.
Example on jsFiddle
So, I would grab all elements:
var elements = document.getElementsByClassName("square");
Then I would create an array with the IDs
var ids = [];
for (var i = 0; i < elements.length; ++i)
{
ids.push(elements[i].getAttribute("id"));
}
And then generate random numbers on the length of the array
var random = roundingFunction(Math.random() * ids.length);
Then retrieve the element at the index and remove from the array
var elementID = ids.splice(random, 1);
And repeat.
There are bascially three different approaches:
Which one would be the most efficient can't be answered in the scope of your question. The difference between them is so small that it negligible considering how much the performance differs between browsers.
If you really need the most efficient, you have to try them all and test the performance in a wide variety of browser.
Otherwise just pick the one that seems easiest to implement. The are all good enough for any normal application.