Here's an excellent analysis of the differences between Nielsen and comScore from Wall Street Journal "Numbers Guy" Carl Bialik, who explains numbers better than anyone.
Nielsen and comScore are fighting to be the primary provider of web traffic counts, the currency currently used to make decisions on many things from advertising to market valuations.
However, both companies use panels. "One concern about online panels, as mentioned in the past, is that those who volunteer may not be representative of Internet users as a whole," Bialik reports.
Nielsen just increased the size of the panel and comScore is starting to incorporate self-reported traffic from publishers.
Regardless, neither company – or any other third-party vendor – will ever be able to provide the detail needed for internal strategic planning and decision-making.