How would I go about having pages removed from not just google, but yahoo, msn, etc. Seems that my website did not have an index page, so when the search engines came in, they ended up seeing all the folders and indexed pages that really weren't meant for public consumption. I've obviously put the index.html in the folder where it was missing, but I'd like to get the other pages removed. Any thoughts?
using robots.txt you should add: User-agent: * (all robots) Disallow: /foldername or filename. You can read more at http://www.searchtools.com/robots/robots-txt.html they have a pretty clear guide there.
Definitely use the disallow in robots.txt but I strongly suggest that you also add the robots meta tag with "noindex" to your pages if it is feasible for you. Believe it or not, disallow pages can actually still appear in the SERPs! Here's a bit more info on that: Robots.txt Disallow
Google allows you to submit pages for removal, but it does take a few weeks for them to look at them. You could do this in conjunction to the robots.txt and 301 redirect.
the best way for not being indexed by search engines is using robots.txt file like mentions above. you can also add noindex tag in your meta tags as an alternative