Virus & malware infected websites
This goes without saying, but any link from another website that is infected with a virus or malware should be removed or disavowed. Perhaps the only exception to this are high profile linking sites that are temporary suffering from such an issue and are expect to be clean domains relatively soon. Note, it is not uncommon for high profile websites to suffer from such issues. Sometimes this can be due to a poorly configured (hacked) server, but often a warning can be generate by third party scripts active on the host sites. There have been a number of instances where advertising scripts have been compromised and spread their infection to other (high profile) websites that utilise their platforms.
There are a number of different ways to check to see if a site contains viruses or malware.
Firstly, utilise the Google Safe Browsing diagnostic page to check for any issues from the past 90 days – http://www.google.com/safebrowsing/diagnostic?site=spamflag.com. Google will also warn you that a site is infected before it will allow you to visit a website found within its search results. Google your sites domain and check the homepage for any issues. Google will also list a warning message under sites it believes are infected.
Both Google Chrome and Firefox will also warn you that a site is infected when you attempt to visit the URL. <SCREEN>
There are a number of online tools which will scan your website for any known exploits, malware or virus issues.
Note, none of these tools are infallible, though you can be mostly certain that a site is not infected if it passes all of these checks.