Use Yahoo site explorer only. if you want to go for paid tool then you can go for the "opensiteexplorer.org"
If you want to try with the paid version than SEO SPYGLASS is very good. though i am not sure upto what limit it has got regarding the number of backlink it will show
Hello, Go to yahoo.com and type the following code: link:http://www.yourdomainname.com It will show you total number of pages and all the backlinks (Inklinks) including the links from the same domain and sub-domains. There are also drop-down of 'show inlinks' available from where you can select the option of 'Except from this domain' and it will only show you the links which other sites are providing your site. This method is accurate and will always be valid. i have been using it since I was a newbie to internet and SEO. As far as TOOLS are concerned, I think there is no such tool which can actually tell you your inlinks. Even I used http://backlinkwatch.com/ for example but it showed me only 100 links (though the link info and links are absolutely accurate).
Yahoo! Site Explorer is the best choice.. Backlinkswatch.com is also good but Yahoo! SE is better than Backlinkswatch. Just go to http://siteexplorer.yahoo.com and put your link in the format: http://www.YourSite.com and hit Explore URL button. Wait for your results and click on the Inlinks button.
Since just about all the people in this thread recommended backlinkwatch, it must be really good. Me, I try not to bother too much with the minutiae of backlinks. Don't want to spend the rest of my life counting and staring at backlinks to my sites.
Which one shows the actual number of backlinks? Backlinkwatch, yahoo site explorer, google webmaster center, google search site:yoursite.com , all shows different numbers.