Online site metrics are very much like online email panels as used by the market research industry. There is much controversy over the quality of panels, the practice in how they are used, and the methodology on how they are recruited. Generally research email panels hold a dark reality that many know of or suspect, but since there isn't a true alternative (or at least a transparent one yet), the industry has to make do with what it has.
For everyone's sake, be transparent in what you do, how you do it, and why. In terms of web analytics, Michael Arrington makes a great call to open Google Analytics completely and notes how "transparency is a good way to gain the trust of the community".
Believe it or not but sharing of data helps stimulate activity and more and more, secrecy around data metrics raises suspicion that something is being hidden. Praise to Quantcast and GetSatisfaction who are, both in their own ways, helping to open up data and make it public.
There is definitely a place for panels but the reality is that whether it is an email panel, a web metrics panel or any other, their job will only get tougher as data becomes available more and more on a public basis - that is unless they can too become more transparent.
What do you have to hide anyway?