I have been checking my own web site with a link checker - to be specific, with Xenu Link Sleuth, http://www.snafu.de/~tilman/xenulink.html

A problem that arises if this is done in a straightforward way is that because the faqomatic URLs produce redirections to their corresponding cached pages, the link checker report is overwhelmed with these redirection reports (which are of course intentional and harmless) and it's hard to spot the remaining cases where a redirection was not intended would better be corrected in the relevant web page.

I have therefore adopted the following procedure, involving two separate runs of the link checker.

1. Set the link checker's options to tell it not to follow URLs that are in the faqomatic. Run the link check starting from the site's home page. Inspect the report for defective URLs as well as for redirected URLs, and fix the site as appropriate.

2. Turn off the option for ignoring faqomatic URLs, and run the link checker starting from the top of the faqomatic.

Inspect the report mainly for defective URLs. Most of the URLs listed in the redirection report will relate to the faqomatic and can be ignored.

This works well enough. There's still a risk of missing cases where the faqomatic pages make reference to some external URL that is being redirected, but redirected URLs are relatively harmless and will probably get noticed sooner or later anyway.