|If you find a GOOD way of protecting the file that stores the passwords, this would be the way to go. But, since just that does not work on Windows, I would not even try.|
So, other ways ... you could write your script, with the passwords hardcoded in it, but then convert your BAT/CMD file to a COM file. These COM files are binaries ... and they COULD distort the hardcoded password, so it would be unreadable. Lookfor BAT2COM or CMD2COM in Google.
Another way would be to scramble the file that stores the password, and let the script that reads the file, unscramble it while reading. The problem is that the file (storing the passwords) may be unreadable at first, but any half-programmer will find out how to decode, since that is stored nicely in the main script. If an additional password is needed, it will also be stored there even ... back to square 1.