Assuming a lot of sites link to www.domain.com/stuff/name.php Would your PR link juice be given to the main url www.domain.com or www.domain.com/stuff/name.php
The pr goes to the exact page where you have links for, in this case www.domain.com/stuff/name.php Of couse, if www.domain.com/stuff/name.php links to www.domain.com, you get some pr for it too.
The above is all true, however I'm not 100% sure of how strongly domain.com would get PR (if a file 'under' it gets PR)?