Most webmasters use Google Webmaster Tools (GWT) to submit their URLs to Google. Yahoo had a similar product – Site Explorer and Microsoft too has one. GWT by far is the best and is far ahead of the so-called competitors.
GWT gives a good insight into what Google sees in your site. They have a module for deletion of URLs (individual pages, directories and entire site). And Google deletes them within 24 hours.
You can submit URLs in bulk by submitting your sitemap but don’t have any means to delete multiple URLs in one shot 🙁 Very painful.
GWT gives a very good report of the dead URLs (404). All they had to do was to allow the webmaster to select the URLs in that report (checkbox) and hit a “Delete Now” submit button. That’s it. I am sure every webmaster would welcome that feature.
Deleting Via Robots.txt
Yes, one can delete URLs through robots.txt but I have found it more useful to block search engines from crawling those listed URLs. It takes forever to remove the URLs from Google’s index (via robots.txt route) and you don’t receive any sort of confirmation after the URLs are deleted.