If you have the space on your external hard drive, I recommend using some backup software such as SuperDuper! which will make an exact mirror of your primary hard drive and also make it bootable so that if your primary hard drive dies, you can just plug-in your external, boot from it by holding the Option key when your computer boots up, and you’ll be right back in business exactly like your computer was the last time it was backed up. You could also just use Time Machine (included in Leopard) to back up your system, it would find everything you needed and back it up automatically. But that said, the missing information is probably system files, yes. Also library files, things like the music for Garageband loops, etc. Most of the data you are probably concerned with losing will be in your Home folder. But I highly recommend using either SuperDuper! or Time Machine, which will automate the process, make it easier on you, and make sure you get all of the info you need.