I have multiple web applications that are currently using linked ASP.NET sitemaps using the siteMapFile attribute of the siteMapNode elements. This allows us to manage each sitemap in only one location while still being able to use navigation features in the top-level application. Is there a way to do this with the WebUI SiteMap?

I'm not familiar with the functionality you're referring to. Can you describe in some detail what it is you are trying to achieve? Web.UI SiteMap supports binding to one datasource so you'd need to combine them beforehand if you have more than one.