Samuele-
Sorry to hear that the server was down for five days. That's not a lot of fun to deal with.
Here's a great link to an interview by Matt Cutts about Website downtime and how it affects Google rankings:
http://searchenginewatch.com/article/2281151/Matt-Cutts-Short-Website-Downtime-Wont-Hurt-Your-Search-Rankings
Basically, if the server is down for a day, you're fine. More downtime than that, though, and Google sees this as a signal that the user experience might not be amazing.
My recommendations to prevent this from happening again:
1. Back up each site to at least two locations. In the case that a server like this goes down, you can migrate the sites to a different host quickly. Make sure you have the database + the site contents backed up. I recommend backing up locally to a hard drive, as well as another cloud-based site, too. For a critical site, it may be worth having a "hot" backup site that can be pushed live via DNS quickly and easily. For a site with 100+ sites on it, make sure you have a list of all of the sites on the server, and order them in importance of what is most critical to work on first.
2. Make sure that the DNS doesn't route through the server with 100+ sites on it. Use the DNS controls at your domain name registrar, instead. That way you can quickly re-route the DNS to go to a new hosting platform, and not have to wait for the server to come back up.
3. Consider moving to a different hosting platform that has more uptime / reliability. 100+ sites on a server is a lot of eggs in a basket. (Note: I've done something similar in the past, and it's not worth it to have all of those sites sitting together on a shared server. Better to break them up and put them on several different servers if possible.)
Finally, once the site is back up, I'd try to bolster the importance of the site with additional relevant content, inbound links, social media, etc. I might suggest a permission-based email campaign to past customers to bring them back, and let them know about the site outage.
Hope this helps...
-- Jeff