A Google Webmaster Help thread brings up a common question I see from webmasters, publishers and SEOs - why does Google Webmaster Tools continuously show old 404 pages in Webmaster Tools when those pages are either no longer linked to or 404ed.
Google's John Mueller said you don't have to worry about it. He said "Google has a big memory" and often Google will continue to retry the 404ed URLs over and over again, just to be sure. Plus, if anyone on the Internet is still linking to a 404ed page and Google crawls that link, they will try it again.
Having 404ed pages is not something that is an issue by itself. Of course, if the 404ed page shouldn't be 404ed then that is an issue. But if the page does not exist, it should report a 404 error, that is what it is made to do.
Google's John Mueller said:
If we've seen a URL once, we're likely to retry it again and again, especially if we should run across new links to that URL. This isn't something that you really need to worry about, it's absolutely fine and even expected that a website returns 404 for URLs that don't exist. Assuming these are URLs that you don't want to have indexed, then these 404 errors will not negatively affect your site's performance in search. Having 404s is fine.
For more details, see this Google blog post.
Forum discussion at Google Webmaster Help.