Without knowing what apps you wish to run, or what you want to achieve, I cannot answer that. "Best used" for what?
The terminal emulator gives you a linux command line, so if you know linux you know what it can do (though by default you only get a subset of commands - you need to install busybox to get a more complete set, which requires rooting the phone). If you don't, then one of our members posted a short list of commands and what they do here: http://androidforums.com/devour-all-things-root/426253-linix-unix-terminal-commands.html
In addition to the general Linux/UNIX commands, I also found a thread that details some of the more Android-centric commands. Keep in mind that all of the commands may not be available to you depending on your device, Android version, root status, etc.
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