http://www.google.com/webmasters

Webmaster console is a reputable source for backlink checking.

2. Yahoo SiteExplorer

http://siteexplorer.search.yahoo.com

You can see up to 1000 backlinks for every domain but results include nofollow links as well. You can also export backlinks to TSV file.

3. Google link command

Using the link command with your website name can return backlinks for a site. Users report that the number of links to websites using the link command in Google is usually less than the number of links seen in Google webmaster console.

link:www.yourwebsite.com or link: yourwebsite

4. Google Allinanchor command

Using the allinanchor command with your website name can return a lot of backlinks for your site. This method may return links which were not reported by the google link command or yahoo siteexplorer.

allinanchor:www.yourwebsite.com or allinanchor: yourwebsite

One disadvantage of the allinanchor command is that if a website name is a generic phrase, results may contain text that are not links.

5. Backlink Tools

http://tools.seobook.com/backlink-analyzer, http://www.seoelite.com

These tools usually compile a report of backlinks along with other useful information like Google Pagerank, Alexa rating, etc.

6. Alternative search engines

These search engines give information about backlinks:

MSN – uses link operator like G or Y – link:http://www.yourwebsite.com
Exalead – uses link operator like G or Y – link:http://www.yourwebsite.com

7. Google alerts

http://www.google.com/alerts

Google Alerts can be configured to check domains periodically and send a notification email when a link is located on the web. This will detect most new links but the tool also locates pages where only a domain is mentioned but no real link is present. Google Alerts are not considered to be extremely accurate and some errors have been reported.

8. BacklinkTracking.com

http://www.backlinktracking.com

This tool reports daily how many new backlinks have been indexed by Google for a given domain. The tool can verify links, detect no-follow status and calculate pagerank of pages.

9. Backlink Watch

http://www.backlinkwatch.com/

This tool has an excellent reputation among the SEO community. It returns up to 1000 backlinks, checking for PageRanks, nofollow and other attributes.