How to use /etc/paths.d to add executable files to my path?
Have you started a new login shell since adding the new file for ImageMagick? The setting of the path from paths.d entries is done in /etc/profile and /etc/csh.login, so you need to start a new shell for the new entries to take effect.

OS X uses path_helper to set the path based on the files in /etc/paths.d - you can always call it manually (assuming a Bourne-like shell here):

$ eval `/usr/libexec/path_helper -s`