This may be obvious to many of you but hosting bad sites on your own domain name is not a good idea.
I.e. if I allowed someone to put a site on http://badsite.seroundtable.com/ that would be a bad thing not just for badsite.seroundtable.com, but it would be bad for www.seroundtable.com. Or it potentially could be.
A Google Webmaster Help thread has Google's John Mueller saying just that.
With regards to other websites hosted within your website, Googlebot doesn't differentiate between accidentally hosting that kind of content within your site and doing it on purpose. If those are really sites that you do not want to be associated with, then I'd recommend making sure that they are not hosted within your domain. If those are sites that you want to fold into your main site, then I'd recommend setting up 301 redirects to the new URLs on your main site.
Again, this is kind of obvious to many but sometimes people need a reminder.
Forum discussion at Google Webmaster Help.
Image credit to BigStockPhoto for broken screen