You can use Root-only apps like Titanium Backup, ROM Manager (with clockworkmod recovery), take screenshots from the phone without needing to connect to PC and use ADB, change the CPU values (like underclock it when the phone is sleeping to conserve battery), change the way the Android OS handles memory management to keep more free RAM, change the calender alert tone etc...
I'm sure there is heaps more, these are just a few things I know of, new to this also...