Hi there,
Honestly, the ones to focus on include the title tag, the meta description, and the robots. If you have a non-English language site, then consider the meta content language and meta language tags. The keyword tag does nothing for rankings. In fact, the meta description impacts rankings very little as well, but assists in providing a marketing message in your search result that can impact a click through to your site. The title tag is probably the most significant on-page ranking factor, so pay special attention to how those are executed sitewide.
Here is a good review in Webmaster Central : http://www.google.com/support/webmasters/bin/answer.py?answer=79812
Hope this helps!
It's only three links. I would be very frank with this client and let them know of the situation, however, but explain how you plan on addressing it by organically creating better links that will pretty much bury any red flags. Any communication you can provide is he best course of action for a healthy client relationship, in my opinion. And if something does happen, there are no surprises. Unfortunately, if the client feels you need to address these links, the only thing you can do is reach out to the sites where the links appear and ask directly to remove them. Good luck!