I'm on a shared server (via LunarPages), and I also host a few low-impact sites for a few small businesses. I recently had a problem (blocked crawlers by messing with the internal settings) that made the sites unable to be indexed by search.I  have since removed the directory restrictions and let search crawl my entire site, but I do not want these other sites to be seen as parts of my main site. (in other words, jojo.com should be jojo.com, never mysite.com/jojo)
What's the best way to handle multiple sites on a shared server?
search engines;indexing
You have multiple options: Use Rel Canonical on your pages, this ensures Google will never index a page on the wrong URL and Domain, I personally favor this out of all options.Use a redirect when a user or bot visits the URL and then forces then back to where they should be, this can be done using htaccess or the httpd.conf Upgrade your hosting.Separate your hosting.Rel CanonicalSimply using <link rel=canonical href=http://www.example.com/pagename/> on your URLS will prevent duplicates entering into Google, Very simple but very effective..htaccessUsing a htaccess such as:RewriteEngine OnRewriteCond %{HTTP_HOST} !^www\.wrongdomain\.com/subfolder/RewriteRule .* http://www.right-domain.com/%{REQUEST_URI} [R=301,L]Upgrade your HostingAlternatively you could always upgrade your hosting to a WHM Cpanel or Plesk account that makes new users rather than new sites meaning that you get an extra layer of protection. This basically jails each site and malware, viruses and exploits are harder to leak though to the other sites. From a security stand point, this would be your best option. Most Hosts provide this but don't advertise it.. worth checking out.Separate your hostingFinally, if upgrading your hosting is something your interested in then it might be worth also considering using a 2nd host, nowadays its so cheap to find a host that only costs a few bucks a month and having 2 web hosts isn't a bad thing in fact many people believe it more solid for creating a back link to your other site (though some argue about C class, and not going there but ya..). 