There seems to be a trend towards using floating layers instead of popup windows. Floating layers (sometimes called "Div Popups" or "Floating Divs") are just HTML elements, such as a divs, styled to sit on top of the rest of the page. It's basically like a real window, and usually they are designed with an X in the top-right corner to let the user close the "window" (i.e. hide the layer).

There are some things to consider when deciding to use floating layers:

1. Popup blockers don't block them
2. People have to look at them at least to figure out how to close them
3. If the user clicks a link on the page, the floating layer disappears with the rest of the page
4. JavaScript is required to close them, but not necessarily to display them (popup windows require JavaScript for both)
5. They will never look or act like real windows on every computer
6. There is usually no way to minimize or resize them, or to switch back and forth between windows

If you think about it, each of these points could be a positive or negative. If you're displaying advertising, you'll be glad to sneak around popup blockers and force people to look at the thing. If you're designing a user interface, you might want to let people minimize, move and resize the popup window so they can see what is behind it.

From a usability perspective, floating layers are a bad idea. You have to design a way to close them, maybe even to move them around. But however you design them, they won't match everybody's desktop. Sure, you can design them to match the default Windows XP theme, but they will stick out like a sore thumb on Mac OSX. By using floating layers, you make people have to stop and think and figure out how to close the thing, whereas they would automatically know how to close a regular popup window without thinking.

There is already a very easy way to make a window that fits in with the rest of the operating system that can easily be moved, resized, minimized, maximized. Unless you have a strong need to use a floating layer, you might as well stick with window.open.