Google webmasters only reports 800 backlinks, months ago I had over 4000 It is as if they removed all article directories I had submitted to.
I've noticed massive fluctuations with google backlinks as well - they seem to come and go even though they've been there for months - did you do something blackhat?
Google webmaster tools isn't showing nearly as many links as they used to. But... I don't know if these means Google isn't counting them anymore or if they're just trying to keep more of the links hidden from view. Matt Cutts has said before that webmaster tools only shows a "sample" and that even if its being shown there, that doesn't mean its counted toward rank. So... I wouldn't worry about it. If you want a more accurate picture of your links, check out Yahoo or one of the other backlink explorers out there. Google has never been very open about that kind of thing.
I agree with these guys that it seems that Yahoo can provide you with a more accurate list of backlinks. Even bing has a more accurate list than Google
the Google webmaster tools is now filtering and not counting a lot of sorts of back links (simar backlinks, social bookmarks..)if they use the same descriptions they may not count them, anyway as long as your rankings are not affected, there is nothing to be worried about.
When you want to check your backlinks, try to check with Yahoo Siteexplorer or Backlinkwatch. They provide better checking compared to google. I always notice a huge difference between google backlink and other site backlink checker.
Google purposefully don't show you all your links so that no one else can reverse engineer your success