Jquery creating checkboxs dynamically, and finding checked boxes

It would be best to give your dynamically injected checkboxes a class to target them better, but based on your code try:

$("#subjects").on("click", "input", function() {
    if( $(this).is(":checked") ) {
    // do something
    }
});

Since your input elements are added dynamically, you need to use jQuery's .on() function to bind the click event to them. In your case you need to use .on() to bind to an element that exist in the DOM when the script is loaded. In your case, the element with the ID #subjects.

This note from the docs is mainly for machineghost who downvoted my answer for no apparent reason:

Event handlers are bound only to the currently selected elements; they must exist on the page at the time your code makes the call to .on(). To ensure the elements are present and can be selected, perform event binding inside a document ready handler for elements that are in the HTML markup on the page. If new HTML is being injected into the page, select the elements and attach event handlers after the new HTML is placed into the page.

$('#subjects input[type=checkbox]').on('click',function(){
    alert($(this).prop('checked'));
});

or the change event: in case someone uses a keyboard

$('#subjects input[type=checkbox]').on('change',function(){
    alert($(this).prop('checked'));
});

simple fiddle example:http://jsfiddle.net/Dr8k8/

to get the array example use the index of the inputs

alert($(this).prop('checked') +'is'+ $(this).parent().find('input[type=checkbox]').index(this)+ responseArray[$(this).parent().find('input[type=checkbox]').index(this) ]);

simplified example: http://jsfiddle.net/Dr8k8/1/

EDIT: Just for an example, you could put the results in an array of all checked boxes and do somthing with that:

$('#subjects>input[type=checkbox]').on('change', function() {
    var checklist = [];
    $(this).parent().find('input[type=checkbox]').each(function() {
        $(this).css('background-color', "lime");
        var myindex = $(this).parent().find('input[type=checkbox]').index(this);
        if ($(this).prop('checked') == true) {
            checklist[myindex] = responseArray[myindex];
        }
    });
    $('#currentlyChecked').text(checklist);
});

EDIT2:

I thought about this a bit and you can improve it by using .data() and query that or store it based on an event (my button called out by its id of "whatschecked")

var responseArray = ['math', 'science', 'technology', 'engineering'];// just for an example
var myList = '#subjects>input[type=checkbox]';//to reuse
for (var x = 0; x < responseArray.length; x++) {
    // here we insert it all so we do not hit the DOM so many times
    var iam = "<br />" + responseArray[x] + "<input type='checkbox' />";
    $("#subjects").append(iam);
    $(myList).last().data('subject', responseArray[x]);// add the data
}
var checklist = [];// holds most recent list set by change event
$(myList).on('change', function() {
    checklist = [];
    $(myList).each(function() {
        var myindex = $(this).parent().find('input[type=checkbox]').index(this);
        if ($(this).prop('checked') == true) {
            checklist.push($(this).data('subject'));
            alert('This one is checked:' + $(this).data('subject'));
        }
    });
});
// query the list we stored, but could query the checked list data() as well, see the .each() in the event handler for that example
$("#whatschecked").click(function() {
    var numberChecked = checklist.length;
    var x = 0;
    for (x = 0; x < numberChecked; x++) {
        alert("Number " + x + " is " + checklist[x] + " of " + numberChecked);
    }
});

live example of last one: http://jsfiddle.net/Dr8k8/5/

The general pattern to do something when a checkbox input is clicked is:

$('input[type=checkbox]').click(function() {
    // Do something
})

The general pattern to check whether a checkbox input is checked or not is:

var isItChecked = $('input[type=checkbox]').is(':checked');

In your particular case you'd probably want to do something like:

$('#subjects input[type=checkbox]').click(function() {

to limit the checkboxes involved to the ones inside your #subjects element.