Javascript Regexp - Match string pattern except if string is inside specified tag

It's not really clear what kind of "HTML" you are working on. If it is HTML code, something from an Ajax request maybe, then you can use a regular expression; matching both a link or the pattern, and then work out what to do in a callback:

var html = document.body.innerHTML;
html = html.replace(/(<a\s.*?>.*?<\/a>)|(\?\?\?([a-z0-9.]*)\?\?\?)/g, 
    function ( a, b, c, d ) {
       return ( a[0] == '<' ) ? a : '<a href="#">' + d + '</a>'; 
    });
context.innerHTML = html;

Conveniently, replace() can take a callback function as a replacement generator rather than a simple string.

If you are working on a live DOM tree, however, you might want to respect events on nodes and not simply reset the innerHTML. You'll need a bit more primitive approach for that:

// returns all childnodes of type text that do not have A as parent
function walker ( node ) {
  var nodes = [];
  for (var c, i = 0; c = node.childNodes[i]; i++) {
    if ( c.nodeType === 1 && c.tagName !== 'A' ) {
      nodes = nodes.concat( arguments.callee( c ) );
    }
    else if ( c.nodeType === 3 ) { 
      nodes.push( c );
    }
  }
  return nodes;
}

var textNodes = walker( document.body );
for (var i = 0; i < textNodes.length; i++) {
  // create an array of strings separating the pattern
  var m = textNodes[i].nodeValue.split( /(\?\?\?([a-z0-9.]*)\?\?\?)/ );
  if ( m.length > 1 ) {
    for (var j=0; j<m.length; j++) {
      var t, parent = textNodes[i].parentNode;
      // create a link for any occurence of the pattern
      if ( /^\?\?\?([a-z0-9.]*)\?\?\?$/.test( m[j] ) ) {
        var a = document.createElement( 'a' );
        a.href = "#";
        a.innerHTML = RegExp.$1;  // m[j] if you don't want to crop the ???'s
        parent.insertBefore( a, textNodes[i] );
        t = document.createTextNode( ' ' ); // whitespace padding
      }
      else {
        t = document.createTextNode( m[j] );
      }
      parent.insertBefore( t, textNodes[i] );
    }
    // remove original text node
    parent.removeChild( textNodes[i] );
  }
}

This method only touches textnodes, and then only those that match the pattern.