Windows Server 2003 comes witha pre-installed firewall. A firewall is software application or a device that permits or denies traffic to your server based on pre-configured rules. Make sure that your Windows server has the firewall software enabled and that the rules are appropriate to your applications
Run AntiVirus Software
Antivirus
software detects and neutralizes malicious software (viruses, worms,
trojans) that attempt to infect your server. It is essential to the
security of Windows servers and should be installed and running at all
times. A comprehensive list of antifirus software can be found at: http://en.wikipedia.org/wiki/List_of_antivirus_software
Backup Regulararly Keep Windows Up to Date Keep Applications Up to Date
Backups
should be conducted regularly, preferably daily, and stored on a
separate location such as Codero.com's Smart Backup service. This not
only protects against data loss but it provides options when data
integrity is compromised (e.g. a mistyped database command).
Microsoft releases important security and stability updates on the second tuesday of every month. Visit http://www.update.microsoft.com/windowsupdate/v6/ montly to keep Windows up to date, or configure Windows to update automatically using the Windows Control Panel.
Dont forget to check for updates to other software installed on your
dedicated server. These can be found at the software vendors' Website
and should be included in your regular patch/update schedule.
Above all, make sure you are writing secure source code for your Website(s). See http://www.owasp.org/index.php/Top_10_2007 for a list of the most common Web Application flaws that can be exploited maliciously.