/etc/paths vs /etc/paths.d

I am curious what the purpose of the directory /etc/paths.d is. My path looks like this, first four set on /etc/paths, the last one on /etc/paths.d/50-X11
echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
This is all done by Apple (Lion).
I am asking because I need to move /usr/loca/bin ahead of /usr/bin, which works fine if I edit /etc/paths. Adding to /etc/paths.d would not work for me as it seems entries in paths.d come after those in paths.
My question is which is the safest & most robust way to add to the path, systemwide (not just a .profile, etc in my home directory).  I plan to start installing lots of 3rd party software and I do not want to let them touch /etc/paths. 
Thank you

Yes, I was able to override the emacs that came with OS X with the one I installed in /usr/local by simply editing /etc/paths. I had to do this because the build did not touch /etc/paths, which is a good thing.
I plan to experiment homebrew, macports and such, see which one fits my needs.
I guess I should rephrase my question. I would like to know what is usually done so that I know in advance where to look if a package breaks my path.
For example, I just installed a Python distribution (Canopy) and it put in ~/.profile the line "source path-to-some-script", where the script does something complicated to prepend the Canopy path the existing $PATH.
I am used to simply explicitly prepending or appending paths to $PATH in a .profile or .bashrc, .cshrc, etc file, and all this seems a bit unusual.
Thank you

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