var first = [ "a", "b", "c" ];
var second = [ "d", "e", "f" ];
My output should be
var final=["a~d","b~e","c~f"];
where '~' is delimiter.
Check if the length of both arrays.
See comments inline in the code:
var first = [ "a", "b", "c" ];
var second = [ "d", "e", "f" ];
var len = first.length > second.length ? first.length : second.length;
// Get the length of the array having max elements
var separator = '~';
var final = [];
for(var i = 0; i < len; i++) {
    // If no element is present, use empty string
    first[i] = first[i] ? first[i] : '';
    second[i] = second[i] ? second[i] : ''; 
    final.push(first[i] + separator + second[i]);
    // Add the new element in the new array
}
                        Here is a function for this... you can specify the behavior, if the arrays are not the same length:
function merge(arr1,arr2,delimiter){
  var i,len;
  var delim = delimiter.toString();
  var res = [];
  if(arr1.length !== arr2.length){
    //TODO: if arrays have different length
  }else{
    len = arr1.length;
    for(i=0; i< len; i++){
      res[i] = arr1[i] + delim + arr2[i];
    }
  }
  return res;
}
merge(['a','b','c'],['d','e','f'],'~');
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