Well there is no one tool to see if a domain is banned or demoted by Yahoo, MSN or Google. The best way to check the history of a domain is to use the WayBack Machine:
http://www.archive.org/web/web.php
See if they have some bad content up there in the past.
Also try typing the domain directly into each engine of interest to see if it shows up as a result. If so it is indexed.
Of course a domain can be blacklisted for many other spam reasons, like email spamming.
Lastly if you feel those old pages were "bad" or could be a reason for possibly being demoted, just delete them and make sure you have a 404 error handler for the old visits and start from scratch. I usually go with the 301 redirect method mentioned above if the old content is trusted and relevant to the new website.