When you link to another wordpress site, that site gets a pingback/trackback that you linked to their content. The pingback consists of your blog title. Can you configure the pingback so that instead of using the blog title, it uses the domain name?
if you're using All-in-one-SEO plugin you can set the post's title to display like: Blog Name | Post Title you can also set that w/out the plugin. BUT I'm not sure if that would turn up in the pings/trackbacks.
There are many ping services that can put into WP CMS.... and dont forget to install NoPingWait plugin.. okay ;p