I've been fortunate enough to have first-hand access to the analytics platforms of a number of fairly high-traffic sites (in the tens-to-hundreds of millions of unique visitors per month), and not once did Hitwise, Alexa, or any of those estimates come anywhere close to actual data. There was nothing shady about the way these sites got their traffic–the vast majority was organic, because they're sites everyone here has heard of–but for some reason the third-party data was just bogus. Like, not unreasonably outside the realm of totall-made-it-up bogus.

It's worth remembering that sites like comScore, Quantcast, Alexa and Hitwise derive a solid chunk of their business by enabling Google sales reps to better convince clients to spend more money. It's not far off from an academic whose career depends on grants by parties who are heavily invested in seeing a particular outcome.