Q:

Added value of Windows Server 2008 over 2003 in terms of security

What is the added value of a Windows 2008 Server over Windows 2003 in terms of security? 
Does Windows Server 2008 has enhanced/new security features compared to 2003?

A:

There's a lot of added value in Server 2008 as compared to 2003. You can, roughly speaking, think of Server 2003 as "XP" and 2008 as Vista. In which case the following are notable changes that impact security:

UAC, UIPI are brought in in Vista. That is, Administrator users are handed two authentication tokens - one with full admin privileges and one with filtered privileges (standard user privs). This is what explorer starts with, thus, most apps are run as a standard user by default, even on an admin account. UIPI allows these windows to share a desktop whilst theoretically keeping them isolated.
Address Space Layout Randomisation. Vista got a full implementation of this.
Proper logon credential handling - whereas previously one could totally re-write the logon dialog with a GINA, now you install credential providers. Risk of intercepted passwords is thus decreased.
In 64-bit versions of XP and Vista, Kernel Patch Protection. Prevents rootkits from hooking interrupt tables by force-bluescreening Windows if they do. Very handy.
A series of protocol improvements were introduced, possibly most notably SMB 2.0.
and so on...

The Vista kernel and operating system was in many ways a very audacious release, containing a whole slew of additional features. There really is no reason to stay on 2003 if security is your end game.
That said, if you're considering an upgrade, practicalities come into play. Server 2008 R2 is already in production use and Server 8 is not that far distant either. I wouldn't upgrade to 2008 given the choice of R2 or Server 8 - I'd be inclined to wait for S8.

A:

In addition to the elements that @ninefingers mentioned, there's another aspect of Server 2008 which could be of use which is the release of the Server Core edition, which gets rid of a lot of the default install (eg, no web browser installed) and thereby reduces the attack surface of the server, if it's used.

