Testing quicksort user input
Spaces

Put a space after for and if:


for(int i = 0; i &lt; bound; i++) --> for (int i = 0; i &lt; bound; i++)
if(giveOutput) --> if (giveOutput)


Put a space around a -:

sample.length-1 --> sample.length - 1

And the same goes for +:

System.out.println("Average time taken to sort array: "+totalTime/bound+" nanoseconds");


becomes:

System.out.println("Average time taken to sort array: " + totalTime/bound + " nanoseconds");


if-statements

Add braces around if-statements:

if (giveOutput) {
    System.out.println(Arrays.toString(sample));
}


Avoid nested if-statements such as:

if(checkCorrectness)
    if(!isSorted(sample))
        System.out.println("WARNING! mistake detected");


Change that to:

if (checkCorrectness &amp;&amp; !isSorted(sample)) {
    System.out.println("WARNING! mistake detected");
}


(Consider throwing an exception for this by the way. A mistake is important stuff)

Naming

Whatever qs is doing (A quicksort I guess), the name is too short to be meaningful. Name it quicksort instead.

Name your methods for inputting things as input*:


getNumber --> inputNumber
yes_no --> inputBoolean



  Are there any guidelines to follow for when prompting the user for information? One thing I'm not sure about is when to prompt with a question mark vs a colon (e.g. "what is x?" vs "input x:").


I believe this can be answered better on User Experience. They probably have a question about it already.

I would think that a question mark should be used when asking a question, and a colon should be used when encouraging the user to enter something. Of course this doesn't say much though as all your user prompts can be modified to the other form. My opinion is that what you currently have is good though.

Other comments


Good choice to use System.nanoTime();
To make the existence of another line in your output clear, I would change System.out.println(Arrays.toString(sample)+"\n"); to:

if (giveOutput) {
    System.out.println(Arrays.toString(sample));
    System.out.println();
}

In Java, the convention is that { goes on the same line, not on it's own line.

public static int getNumber(String message)
{


should be, according to the conventions:

public static int getNumber(String message) {

Avoid multiple variable declarations on the same line

long totalTime = 0, sumArraySizes = 0;


can be:

long totalTime = 0;
long sumArraySizes = 0;