That's an interesting question, because a GNU/Linux system will typically contain hundreds, perhaps even thousands of utilities. It's virtually impossible to learn them all
The official Debian docs would be a good place to start, although admittedly they might seem quite overwhelming at first. See
here.
The best way
in my experience to learn a new operating system is to literately just throw yourself into it for a couple of days/weeks, learning utilities as and when you need them. Just make sure you have another desktop or something available to look up things when you get stuck.
One utility that's very useful to know about is "man". By typing something like "man cp" you will see documentation for the copy utility. Nearly every package you install will have a man page to read
If you haven't yet received a Raspberry Pi and would like to learn the Debian environment, then perhaps consider installing Debian in a virtual machine?