I promise you I'm not a spammer

There are quiet a few websites that allow you to check which links a competitor has. It's also important to check your own site - you may think you have 100's of links but Google and Yahoo treat them in different ways so you might have a very high rank of Yahoo and a low one on Google as it's only registered a few of your links.... I'm still figuring all of this out.
Can anyone clarify why Google doesn't register the majority of links, while Yahoo does?