[aphyr]

Impact factor (# of citations per article in journal) tends to be lower for free journals, since a.) the threshold for publication tends to be lower, and b.) the established journals still have prestige, which largely remains the currency on which scientific reputations and tenure are built. Because most of the big journals don't allow you to retain publication rights after publishing with them, anyone who does big-impact research worthy of publication in those journals faces an exclusive choice between prestige, exposure, and selectivity, or opening their work to the public at the cost of "devaluing" their work. It's a real dilemma--one which publishers are trying to exploit for all they can.

The picture is changing (look at the amazing success of the Arxiv), but I think for-profit, paywalled journals are going to be alive and kicking for quite a while.