The DirectoryIndex command gives Apache a list of files to check for. It displays the first one that exists, and only if none of them exist does it generate an index of files.
Something like this would work.
DirectoryIndex index.html index.cgi /missing.phtml
As far as I know, there's no limit to the number of filenames you can list - but how many different extensions do you actually use?
On some of my websites, I use
DirectoryIndex index.html /index.html
so that if I haven't an index.html in a subdirectory, it takes them back to the home page without explanation. That's not necessarily polite, not giving an explanation, but is unauthorized snooping polite? I figure I would notice if the index.html was missing from the root directory, but I could lose a /missing.html file and not realize it for months. Maybe you'd want to have the /missing.phtml followed up by an /index.html, just in case....