hi,
we had an agency check our site with a tool that shows us that out of say 1000 backlinks 170 of them have suspicious anchor text. digging a little deeper we saw that most of the anchor text was our company name, the next highest was our service. then i checked another site to see what type of sites were linking to us using those phrases and most of them were reputable domains like dmoz etc... so how reliable are these types of warnings and how can you tell if a link is "bad" webmaster tools has not given us any warnings yet for bad links etc..