our makes a lexically scoped alias to a package variable. So,

package B;
our $d = 1;
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means that for the rest of the lexical scope (in your case, the current file (and of course not if it's hidden by a definition in an inner scope)), $d is an alias to $B::d. So, your code is equivalent to:

package A;
package B;
$B::d = 1;
package C;
package D;
print $B::d;
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Don't worry if you find it confusing; many people do. Luckely, you don't have to use it. I find myself using it only for variables like @ISA and @EXPORT.