I'd guess that blackhats and whitehats are all out building those lists of vulnerable machines. They can then go back and exploit them en masse later.
There aren't going to be that many popped servers because the number of Internet-facing web apps that use CGI + have bash as /bin/sh or call bash explicitly is not all that high, though it is still high enough to build a considerable botnet. The other issue is that they need to find a code path in a CGI app that calls out to bash, while many of the bots so far seem a bit naive in their crawling (excluding the ones targeting specific appliances and panels). A request to a hypothetical /cgi-bin/status.cgi may not do anything, but what they don't realize is that status.cgi?details=1 may call system("date") and then give them RCE.
However, CGI isn't common these days. I don't know any large sites still using it.
So it's mostly going to hit older sites that work but aren't well maintained. Also a lot of embedded systems have CGI based web interfaces that could be vulnerable. It's not clear what the effect of that will be.
It absolutely is a problem for many other things, but non-CGI web apps is almost always not one of them.
See Per-Request Environment Variables at http://www.fastcgi.com/devkit/doc/fastcgi-prog-guide/ch1intr...
These aren't ubiquitous---but it also isn't just CGI programs that expose this vulnerability.