One on my favorites and most useful has to be the search functionality. To use this simply hold down CTRL + R in your Terminal or Command Prompt and type in a character and you will see entries from your history, keep entering characters to narrow down your search.
Human readable sizes
ls with the -lh option, shows sizes in human readable format.
Clear current window
Simple way to clear your current window, use this to make visualizing terminal easier.
Show hidden files
When using list you can add a -a to show hidden files and folders.