How do I use the command line options to make Toad do something every night?

You can use the Automation Designer in Toad to schedule many, many tasks within Toad. Please see the online Help within the tool, and there is a video describing the process here: 

For any of the windows that support command line execution:

1. Go to the window and set your options as if you were going to run the window now.
2. Click the "save settings to file" button (floppy disk icon).
3. Open up the file you just made with Notepad. There are directions in it on how to do the rest:
   1. The directions show how to call TOAD from the command line with this options file.
   2. If you want TOAD to close after it runs, uncomment "CloseTOAD"
   3. Depending on which window this is, there may be other things you need to specify, and they are described in this file.
   4. If you want this to run nightly, you can make a batch file with the appropriate command and then schedule it with your Windows scheduler.