After reading up on Jakob Nielsen’s alert box, it appears he agrees with you as well:

http://www.useit.com/alertbox/open_new_windows.html

Here’s what Jakob has to say about it:

“Because users frequently close document windows, the best guidelines for linking to non-Web documents are:

1. Open non-Web documents in a new browser window.
2. Warn users in advance that a new window will appear.
3. Remove the browser chrome (such as the Back button) from the new window.
4. Best of all, prevent the browser from opening the document in the first place. Instead offer users the choice to save the file on their harddisk or to open it in its native application…”

I think this is best for the majority of users, and power users can just override the browser’s new window functionality.

Incidentally, to override target=”" links opening in a new window in Firefox, you can tweak the browser.link.open_newwindow setting in about:config — setting it to 1 opens target=”" links in the current tab, setting it to 2 opens them in a new window and 3 opens in a new tab (default).

That being said, I appreciate that we sometimes must compromise for a client and your solution certainly is clean and to the point.

Which particulars of your code are specific to MooTools 1.2? I’m going to write a series of articles comparing differences to the MooTools codebase between v1.11 and 1.2, and am curious if you’re using any 1.2-specific functionality in this code.

Here’s the first article I wrote, which contains a brief overview of the additions/changes in MooTools 1.2:

http://www.thetruetribe.com/2008/06/whats-new-in-mootools-12.php

Your method is just like adding the target attribute inline, which is not standards compliant.

So you could do something like this instead:
el.addEvent(‘click’, function(e){
(new Event(e)).stop();
//plugin your own code in the open function.
window.open();
});