If your using wordpress it already has a native ping to search engines for top level and articles.
When link building it is best to keep in mind relevance to content on the page. For general directory or top level concepts submit for example you have a Gardening website, submit your Organic category to organic related gardening sites, Garden tools, to the garden gadgets listings. You can also use this url method when commenting on blogs relevant to the topic.
Meaning in the signature area use the appropriate URL to top level category.
Page specific gets automatically submitted on post by default in wordpress (pingomatic typically)
Utilize your social networks ie twitter, facebook, delicious, digg, technorati pages to broad cast specific urls.
Hopefully you have the "sexy bookmarks" plug in to allow your readers to help you with page specific bookmarking and sharing which will help you.
Also, another tactic is to guest post or share a specific article with a complementary with your topic site.
As always in link building use your long tail keywords -that are relevant to the page topic ex: "10 top gardening tools" as your link vs. www.mywebsite.com/garden-tools.