Filter TinyMCE config to make new pastes default to have links open in new window.

filter_wp_pastes_to_make_links_open_new_window.php

<?php
    function format_tiny_mce_pasted_links_with_blank_targets( $in ) {
        $in['paste_preprocess'] = "function(plugin, args) {
            var temp = document.createElement('div');
            temp.setAttribute('id', 'temp');
            temp.innerHTML = args.content;
            var linkList = temp.getElementsByTagName('a');
            for(var i = 0; i < linkList.length; i++){
                if (undefined != linkList[i]){
                    linkList[i].setAttribute('target', '_blank');
                } else {
                    break;
                }
            }
            args.content = temp.innerHTML;
        }";
        return $in;
    }
    add_filter( 'tiny_mce_before_init', 'format_tiny_mce_pasted_links_with_blank_targets' );