Here are the following process for each search engine’s ie;Google,Yahoo and Bing.
For Google.com:Simply go to Google and type in “link:example.com”,take a look I did it for “http://timesofindia.indiatimes.com/”
For Bing.com:Simply go to Google and type in “inbody:example.com -site:example.com”,take a look I did it for “http://timesofindia.indiatimes.com/”
Here are most simplified manual command we can type in to major search engine’s to find out the no. of backlinks counted by corresponding search engine for a specific website,I think those manual commands are much better than any free tools.But for an information, those command wont return you the exact no. of back-links,the simple reason is nobody will disclose their whole algorithmic linking structure to avoid search engine gaming.