I have been publishing scientific manuscripts for the past 22 years. My educated comments with regard to journal impact factor has always been the same (If you do not know what JIF is, please have a look at this Wikipedia entry). First order, you should publish in the most important journals for your field. If their JIF are low, who cares as long as your work is important to your field and well cited. For example, the scientific discovery of 2012 according to Science (very high JIF) is the publication of the experimental finding of the Higgs boson… in Phys Lett B (low JIF relative to Science)!
Do not forgot that from an historical perspective, we are awfully bad at predicting what will be the next important discovery down the road. A number of fundamental discoveries and early engineering feats were discarded at first. Similarly there are numerous example of scientists having had tremendous issues in getting those game-changing results published, even those ending up winning Nobel prizes. Karry Mullins’ PCR work is one of many examples of work was rejected by journals having top JIF but for which the application of this very technique was published in Science and Nature and the citations counts of these second generation papers also receiving higher numbers than the original, award-winning work!)
Now, you do not have to agree with this lone scientist opinion but certainly you should have a look at the The San Francisco Declaration on Research Assessment or DORA petition, which is supported by the “big boys” (no discrimination intended). The declaration statement is actually a very interesting read and it covers the historical origin of the JIF (which was not for evaluating researchers at all) and further call for dropping journal-based metrics in assessing scientific productivity for funding and promotion. Over 240 organizations and 6000 individuals have already signed the declaration.
In conclusion, do not loose a good night sleep over your favorite journals’ impact factors…