I've been using Yahoo Site Explorer and Google Webmasters Tools to check link counts. Just started using both in February. Also, I don't have a SOAP API key, otherwise I would look at the digitalpoint tool for comparison. Problem is that both Yahoo & Google haven't budged for 3 to 4 weeks on any dofollow forum signatures I've done. Do forum dofollow links get followed but not counted? Or do I need to be more patient for Webmasters Tools & Site Explorer to update? Is there a better tool?
Webmaster Tools takes ages to update. Sometimes it takes months for backlinks to show up there. Or they just dont show up at all. Do a "site:www.mysite.com" search and see if it shows up on the list - if so, you know it's basically a backlink..
google will take time to show the links. Try yahoo inlink it should show you all the backlinks from dofollow forums.
Every dofollow links counted by Google, Some times it tooks time to show in the link command as well as webmaster tools. Don't worry about it.