I notice that google only reports links to the homepage of a site with the link:
Hmmmm, that's actually not entirely accurate - the link command works for any page. But when you're doing link:www.yoursite.com you're actually doing link:www.yoursite.com/index.html - ie one page (the homepage, which if it's an apache web server will be index.html by default). If you had a page www.yoursite.com/lollypop.html then doing the command link:www.yoursite.com/lollypop.html will tell you the links coming into that lollypop.html page.
But! important caveat! Google's link: command doesn't actually tell you every linking page Google knows about but just a sample of them! And there's no way to do one command which tells you every link into every page - for that use Google's webmaster tools or take a gamble that it's approximately the same as Yahoo's site explorer results.
To see an accurate picture of the incoming links and also to see link for inner pages of your website, you need to create an account with Google's Webmaster Tools service.