As far as I know you will need to use the AppleScript Editor and save it as an Application file format (extension .app). You can save the application program anywhere you like; I suggest in your documents folder. The location does not matter as long as it is convenient for you and you are able to find it easily.
You do not have to create a separate Applescript for every program; instead you can add the same three lines for each program you want minimized. Below I have included three examples, Skype, Google Chrome, and iTunes. I have also added a 15 second delay so that the programs all launch before the AppleScript runs. Without this, the Applescript will try and run before the programs have launched and return an error. You can adjust this value based on your Mac's speed.
Continue creating minimize commands for all of your startup programs using their application name, and then test the program by clicking the arrow. This will minimize the programs you had specified. Then save the AppleScript as an application.
Then go to login items under the Users System Preferences pane, and add your Applescript application. It should automatically run last.
This should minimize the programs you specified next time you login.
I hope this helped!