I also went off a bit on a rant about how this is a big concern for me. I wrote:
Honestly, this really concerns me. Google clearly was using soft-404s behind the scenes for a long time. Providing this data to webmasters resulted in many claiming Google was soft-404ing pages that should not be 404ed. Now, with webmaster feedback, Google can address the issue. This is just concerning.
Now, Googler JohnMu is saying in a Google Webmaster Help thread that there is no penalty for soft-404s. He said:
To be clear: Google will not penalize your site for having soft-404 pages. Having soft-404 pages makes it harder for us to recognize new and updated content on your site, but it does not mean that we would see you site as being any less valuable in the search results :-). There's no need to rush and do something drastic here. Yes, it would be great if it could be cleaned up (that's why we have started reporting these things), but in general, it's not critical.
Honestly, I never thought there was a "penalty" but my main issue is that if Google misclassifies a page of yours as a soft-404, then by definition, Google won't include that page in their index or at least, not rank it well. It is not a penalty, it is just an issue with the page. Now, in some cases, this is the webmaster's fault and in other cases, it is Google's fault.
Either way, this is not a "penalty" but it doesn't lead to good Google search results for your pages classified as soft-404s.
Forum discussion at Google Webmaster Help.