Yes, I can generate a new address through the bitcoin-qt command console, but how might I run a for loop to generate 100 different addresses? What kind of file does the bitcoin client take?
You can't. It only accepts specific API commands as described here or by calling the
help command in that dialog.
Can I run a python script through the bitcoin command console?
If by the "bitcoin command console" you refer to
QT's dialog then no, you can't. You can run a script from your console, though, if you have Python installed in your system or go for a more elegant approach a use a proper RPC API wrapper.
How exactly does sending multiple commands to a command prompt work?
It has already been answer above.