How to execute custom Python code on startup? I understand you can put custom Python scripts in scripts/startup/ and they will be executed upon starting Blender.

However, I need to store my script outside of the Blender installation. With other software, such as Maya and Nuke, I can define an environment variable which will make those apps look for a script in a custom location and execute it during startup. Does Blender have anything like that?

EDIT: I can't open up the Blender UI and change options that way... as I'm talking about a deploy of Blender on many machines in a company. Therefore it has to be something which happens during the startup of Blender.
Go to File -> User Preferences and select the "File" tab. In the dialog, there is a "Scripts" entry where you can define the location of an alternative scripts directory.

If you want to deploy this change to a lot of blender installations, simply copy the userpref.blend file to your skeleton/template user home directory. Whenever a new user is created, this file will then be copied to his home directory, and when he starts blender, he'll have the changed script preference. The neat thing is that you can change other preferences values (and the startup blend file, too, if you want) with this. For Linux, the file lives under ~/.config/blender/blendversion/config/userpref.blend. I'm pretty sure that for Windows there is a similar file that gets stored somewhere in the user's homedir.