A project I left a few months ago still uses CGI. However, the site is for a very small user set (it only has about 40 users, and probably less than 5 use it frequently). While the hardware has been replaced 3 or 4 times, some of that code has been running for almost 10 years, with little or no modification. I'm sure other technologies would provide a performance improvement, but current performance is acceptable, and manpower to make a change is short, spread over too many areas, and not well versed in web technologies (especially since I left). This leads to an attitude of "If it ain't broke, don't fix it!"
As for replacements I've used/plan to investigate: In my new position, I've developed a web app with PHP. However, I'm more of a Python fan and plan to look into WSGI soon. I also plan to use AJAX to replace a CGI program on a site I voluntarily maintain for a non-profit.