I have this not so many checkboxes:
I would do this something like this:
var all, checked, notChecked;
all = $("input:checkbox");
checked = all.filter(":checked");
notChecked = all.not(":checked)");
After that you can use jQuery.map to get the ids of each collection.
var checkedIds = checked.map(function() {
return this.id;
});
var notCheckedIds = notChecked.map(function() {
return this.id;
});