If it's your own website, you can verify your site with google webmaster tools and siteexplorer. Both will let you download TSV/CSV files with your backlink profile information.
Install SEOquake plugin for firefox. It will show you backlinks with their PRs and many other useful parameters.
I like the Firefox plugin the best. It slows down my system a little bit, but it's worth it for the amount of info I get about my sites and competitor sites.
You might want to change your preferences according to your needs. Your speed will increase if you reduce the things it show.
If you watch to check the number of backlinks that Google has found for your website, do link:http://www.(domainname).com
There is not point to search for backlinks on google, as google hugely cuts down amount of displayed backlinks, it's their policy. Yahoo links is the most reliable of free sources
Do use back link watch dot com, I use the same. If it is your own website configure it with google analytics and traverse all you need.
There are several tools to do that but the most easy and the simple way is that you just install the google toolbar and enable page rank in it. Once the toolbar displays on your browser, simply click on the Page Rank button on the toolbar and it will show you the option of checking backward links.