What's the OS? Windows Server 2003 Standard Edition, or SBS 2003?
Even with SBS 2003, which is a LOT busier than most Server 2003 Standard Editions, you can typcially make them function with a 12 GB System partition. I've managed a lot of SBS 2003 servers with that partition size. You relocate things like the Shared User folders, Exchange stores and logs, keep a handle on the Windows Updates Uninstall files, set the System Restore files to a reasonable value, etc.
If you still want to resize, you can use third-party partitioning software. Paragon's server partition manager software will work. It's about $300. An acquaintance used it to expand an SBS 2003 System Partition.
You need to back up EVERYTHING. ASSUME THIS IS GOING TO FAIL. Make a full system backup of the boot partition (including System State) and backups of all your data.
Other software that can handle this include system imaging software: ShadowProtect Server and Acronis Server. You can back up the system drive image, re-partiition the hard drive from Windows setup, and then restore the System partition to the new larger partition. Then copy your data back from your backups of the Data drive.
Heck, even Windows Home Server could do this for you, although it's not supported by Microsoft with Server 2003.