As Eric Schnell points out, although ISI impact factors have been criticized before, a recent editorial in the Journal of Cell Biology addresses the validity of the underlying data.
Now might be a good time to re-visit the h-index, which Scopus employs as an alternate method of estimating scientific impact.
update: SCImago has a new, free journal ranking database. More at Open Access News: http://www.earlham.edu/~peters/fos/2008/01/more-on-scimago-journal-rank-v-impact.html