I usually use Symantec Backup Exec System Recovery to redo partitions. I'll make an image of the system and then restore it to the same drive, modifying the partition size. This method makes the most sense to me, because you want to have a backup of your system before playing with partition tables anyways.
You can also use something like Partition Magic to resize partitions.
Personally, I don't make my system partition for server 2003 any bigger than 20-30 gb. server 03 doesn't need that much and I usually tell all of my server programs to store data on a separate partition. That way if the system has problems and needs to be restored, the data for the programs isn't touched.
My recommendation is to keep the system partition the same size and use the rest of the space for data on a separate partition.