Each URL on your site has its own PageRank. So
http://example.com/?id=344 will have separate PageRank from
http://example.com/ and both will have separate PageRank from
In many cases a URL parameter will not cause the page shown to change, or will cause a 404 not found error. Either of those may cause the link juice from the inbound link to be worth less than it otherwise would be. You can help the situation with URL canonicalization. Either configure your server to issue 301 redirects for such URLs, or use the meta rel canonical tag to tell Google that two pages with similar URLs should be treated as one.
Because you want each of the pages on your site to rank well in search engines (not just the home page), it is very desirable to get inbound links into lots of pages on your site. I would say that inbound deep links are actually more valuable than links to your home page. Getting deep pages to rank well is one of the best ways to get more search engine traffic.
In summary, all inbound links to anywhere on your site can help your "link juice" and your site will rank better because of them. Links into non-existant or duplicate pages should be fixed to point to content at the preferred URL.