**This was written as an email response to someone over a year ago but still stands very true today and will for the foreseeable future**
No third party backlink tracker is at all reliable and can not be used for tracking what links you do have or what links of yours the search engines see, they definitely do not show all of the links you have.
As an example I just did a backlink check on a domain that has been online for about 6 years now, it is one of my main domains that has had periodic SEO done on it over that time. Backlinkwatch claimed 298 total backlinks whereas ahrefs.com claims 1420 total backlinks. Bear in mind that in October last year before Yahoo Siteexplorer was shut down it claimed 20k+ backlinks for that domain when ahrefs was claiming around 1100. This domain probably has closer to 30k+ actual links now.
These sites are all over the place and cannot track your links nearly efficiently enough, they are a waste of time for anything other than trying to find some of your competitors link sources.
For example; If NHSEO has created 1000 links to your website and you can output the list and see that indeed these 1000 pages are linking to your website but the search engines say you only have 50 links who will you believe, your own eyes or the search engines?