Right now I have a 20gb hard drive sitting around doing nothing. I decided that I would use this to back up my home directory. I was wondering if anyone knew a good way to do this. I want to have it back up anything to the 20gb that had been updated since the previous back up in the /home that was under 100mb. I was thinking like setting it up to do this at 4am or so if the computer is on.

Anyone know a good way or program to do this? or Will I have to write some crazy SH script? I am a java programer and have never written an sh script to do much more than download a few things with wget or compile some things.

I use rsync to backup my folders and after the initial run, all other runs just update things so it's very quick. For that reason, I don't even bother using cron for that.

You need to put a partition on the second drive and format it as ext3 for example:
mkfs.ext3 /dev/hdb1

mkdir /mnt/images
mount /dev/hdb1 /mnt/images -t ext3

Put an entry in the /etc/fstab so it's available every time you boot.
/dev/hdb1 /mnt/images vfat defaults 0 0
To make it writable for users with a group id of 500, edit the /etc/fstab file to include the following line /dev/hdb1 /mnt/win vfat gid=500,umask=002 0 0

Run the rysnc job, I usually run it a couple of times to make sure everything went ok.

rsync -av --delete-after /home/fred /mnt/images

Try this:

http://www.rsnapshot.org/

You can control the snapshot interval and how many snapshots to keep, it will rotate the snapshots for you, very handly.

Would there be anyway to exclude files over 100mb with rsync? there is an exclude PATTERN but what is a pattern>?

You could create a list by using find or even putting the files into the list manually. May require some experimenting.
find /home/fred find -type f -name '*' -size +1000 -exec ls {} \; >list
rsync -av --exclude-from='list' /home/fred /mnt/images

Mondo - this is what i use (and many others) to backup my server. By using CRON i can create backup schedules.

You might also want to check out DAR. I searched for 4 years for a backup solution to do what I wanted; I found it with DAR.