We routinely submit (our own as well as clients' sites) to around 1000 directories (or even more) within a month (or even less). We are yet to observe any ill-effects that could be conclusively attributed to these directory submissions/links.
As we know that Google recently update the panda, penguin, over optimization and EMD Update...Now we have to modify our SEO Tactics. It means we have to do the submission as a proper way so that we will get natural back links from directories and articles or other seo tactics...I think we must do Directory Submission (100), 4 Articles Post (40) and other activities in a proper way as it seems natural back links....keep it up