At best, Google and Yahoo Site Explorer only ever show 20-30% of a site's backlinks (based on what they show me for my own sites). SEO Spyglass blows those two away though and every Internet Marketer should be using it.
More importantly, backlinks influence your rankings regardless of whether or not they show up in these inconsistent reporting tools. Many never will.
Bottom line: maintain a consistent linkbuilding regime and watch the SERPs for your ranking movements (assuming you have picked a winnable SEO fight!).
These reporting tools mean next to nothing.