It would seem to me that VirusTotal's success has actually been it's downfall, with service levels reaching epic proportions and as such rendering the service unusable at times, and it would seem this is becoming more regular.
It's always good to have a few alternatives to use, especially when one is down or is experiencing high usage and I've listed a few I've found here .. if you can suggest anymore I'll add them to the list

http://virusscan.jotti.org/
http://vscan.novirusthanks.org/
I did find another two, although the first wouldn't scan the file I submitted and the second one is undergoing maintenance apprently!!
http://www.virscan.org/
http://scanner.virus.org/