Once you build a web part, it's easy to add it to a SharePoint page. Just open the web part toolpane browser and drag it into a web part zone. But what if you want to force this web part on ALL pages that use that site definition? This is similar to to the custom navigation component I built for SPS (plan a post dedicated to it when I roll off my project) that replaces the left-hand vertical out of the box navigation.
By the way, I didn't embed a web part into the site definition pages for my navigation... instead I used a vanilla ASP.NET user control because it was needed in some other non-Sharepoint apps as well.