I know Yahoo always has high link estimates, and Google's links are not updated frequently, but there is definitely something weird going on with one of my websites. Yahoo says I have over 11,000 links, and Google says I only have 5. I have been adding somewhat low-quality links, so that may have something to do with it. I was ranked in the top ten for most keywords in Google half a year ago, then I started adding low-quality links, and I fell out for most of their keywords. I am still in the top ten in Yahoo and MSN. Is it the bad keywords that are causing this, and if so, or if not for that matter, how should I try to fix it?
Yes the major difference between the links that Google and Yahoo report is the quality. Yahoo will report pretty much anything they can find. Meanwhile Google prefers to only report higher quality links. Those low quality links are likely why you lost your Google rankings. You got spammy and lost Google's trust. It can be a long uphill battle to try to get back on Google once you lose rankings.
I have noticed the same with previous clients who think that spamming links is the best way to increase their rankings. Each link exchange you do you should consider the consequences. For example is this going to be help me or is this going to harm my SE Rankings? Look for links that compliment your website so that Google will not punish you.