Within a browser, the content of your web app always has to be contained within a browser window, it can't just float on the desktop, so if you want a completely independent popup, window.open is your only option. GMail chat does still use this - it just uses the window.open options to hide the menus etc.
Depending on how your site works, another option is to create fake windows within an existing webpage. There are lots of existing examples of this. One we have used in the past are RadWindows from Telerik - see the example at
http://demos.telerik.com/aspnet-ajax...defaultcs.aspx
HTH
Phil