What I have is client/server apps that want Windows on both ends. Does OS X have a built-in equivalent to group policy that will centrally manage the hardware settings of the computers, and the software settings of the users, or centrally manage the IPSEC policies of all the machines on the network?
Welcome to vendor lock-in.
Does OS X have a built-in equivalent to group policy that will centrally manage the hardware settings of the computers, and the software settings of the users, or centrally manage the IPSEC policies of all the machines on the network?
Yes, down to the devices and software they can use, and it'll even work if the user has a disconnected laptop. Remember, this is UNIX. It even automates creation of custom images for your clients and will install them over the network (with a filter to make sure images go to the right hardware). It will net boot all your clients, for example if you're running a classroom and don't want anybody touching the local OS. It runs software update server with local cache just like Windows.
Apple sells an application called Apple Remote Desktop 3 for centralized management. It should be capable of performing the tasks you described.
In the Mac OS X Unix terminal, I see man page documentation for ipsec, setkey and racoon, the same software used to manage IPSec in BSD and the Linux 2.6 kernel. ARD supports remote UNIX script execution, so that can probably be used to manage basic IPSec configurations across a network.
Mac OS X also has a built-in L2TP/IPSec client, and it's possible ARD can manage it with a high-level interface like Automator.app, but I haven't tried it for that purpose. Its configuration options are more limited. The configuration panel looks like this -
Apple's Xserve server hardware, running Mac OS X Server operating system, has a complete set of tools for local and remote administration, and lights-out management hardware.