[Vlasenko Fedor]

<script>
var arrF = [3, 5, 8];
var arrS = [1, 2, 3, 5, 8];

function getIntersect(arr1, arr2) {
    if (arr1.length < arr2.length) {
        [arr1, arr2] = [arr2, arr1];
    }
    for (var i = 0; i < arr1.length; i++) {
        for (var j = 0; j < arr2.length; j++) {
            if (arr1[i] === arr2[j]) {
                arr1[i] = arr2[j] = 0;
            }
        }
    }
    return [arr1, arr2];
}

alert(JSON.stringify(getIntersect(arrF, arrS)));
</script>

вариант