BuddyPress.org

This is a problem with regular WP, though. (WP 2.9.2 + BP 1.2.1)

On shifting my WP files from the parent directory (example.com) to a separate WP directory (example.com/wp/), Buddypress URLs contain a /wp/ in them, by default.

For instance, the admin profile url is example.com/wp/members/admin. Manually typing in example.com/members/admin will get you to the same page, without any errors, but all inks generated by BP contain /wp in them.