The funny thing about SharePoint portal server 2003 is the broken links in the sites area when you delete a website from WSS, the link stays in the sites list with a broken URL and you have to remove manually not to mention if the number of sites is large and the websites are automatically deleted because they are not used, you have to start checking links if it is broken or not and then remove it which is a very big overhead 
, they did improve this issue in MOSS 2007 and developed a sites link checker, Check this screen shot for the site menu below.
When clicking the first open scan for broken links, the following screen appears:
When you press okay MOSS will check the broken links and display results as shown below:
Press okay again and a list of broken links would appear, you can delete all the broken links like removing list items 
Enjoy.
yazanouf