Google is now showing soft-404 pages in the page not found error report in Google Webmaster Tools. Google just confirmed this on the Google Webmaster Central blog, and it was first noted in a WebmasterWorld thread early this morning.
I personally tried to verify this, but did not see them in my reports. But Google did post a screen shot:
A soft 404 is a page not found page that returns a 200 status code, instead of a 404 status code. Often, webmasters create custom 404 pages, but neglect to show a 404 header status code. This can cause issues for search engines and users.
So this report is to help webmasters discover this error and fix it.
Forum discussion at WebmasterWorld.