Doesn't Google webmaster tools only show the first 300-500 links or so? The alternative might be to do a quick search in google "links:*domain*"
i don't say that is the best but take a look also to http://forums.digitalpoint.com/showthread.php?t=2049889
I like http://www.seomastering.com/backlinks-checker.php. It's quite accurate in my experience and you can check numerous Website's backlinks.
seems to be ok ! but the capcha is hard very hard to read and msn links need to be changed with the bing ones now!
I'm very sorry to hear that two of you have had a bad experience with the backlink checker I recommended. I tried again and it worked well for me. I'm familiar with other ones as well but for me personally, this one provides more detailed information and that's why this is my preferred choice.
Wow, this thread dates from 2007. Guys to check backlinks you can use seo spyglass or traffic travis. These are both free tools and give you also the anchor text, page rank etc. If you only need to know how many backlinks your site or anybodies site has just go to majesticseo.com or opensiteexplorer.
Ahrefs is definitely the best. Now I use their free account. When I run out of ahrefs limit, I switch to Moonsearch. They have their disadvantages, but they are completely free and show unlimited number of backlinks.