Quick and Dirty
Here is the instructions to do a quick and dirty Heretic II server.  I will be adding to this guide and updating it as I find more things you can do with the servers setup.

Installation
Install Heretic II opting to leave the movies on the cd.  Then you can free up some space by deleting the following directories:

• gamespy
• Help
• drivers
• base\config

If you know of other files or directories that can be safely removed please feel free to let me know.  After clearing out the listed directories I ended up with 251 Meg taken up on the server.

dedicated.cfg
One thing that Raven did with the codebase for Quake II was to make it so that when you run the game using the +set dedicated in the command line it automatically executes the dedicated.cfg file.  So therefore we can take and put everything we would have normally included in a server.cfg for a quake II server and include it in the dedicated.cfg.

Here are the basic ones you will want to add to get your server up and running.   Edit the dedicated.cfg file located in the Heretic II\Base directory and add the following:

set gamespyport 28911
set public 1
set hostname "3DGW Heretic II"

You can set the hostname to anything you would like.  This makes it so you can identify your server in gamespy.

GameSpy
Here is a bit on setting up the server for gamespy that I cut and pasted from Blue's News:

If you want to have your server seen by GameSpy and other Master Server List-based utilities, you need to set a GameSpy port and make your game public. To do so, do the following:

The default port for a Heretic II server is 28910. You will want to set your GameSpy port to that number + 1 with the following command:

In your command line launch or config:
    +set gamespyport 28911
Or in the server itself:
    gamespyport 28911

Next, set your public setting to 1.

In your command line launch or config:
    +set public 1
Or in the server itself:
    public 1

Additionally, you can set up multiple servers on a single machine by changing the port number.

In your command line launch or config:
    +set port 2x910
Or in the server itself:
    gamespyport 2x911

...where 'x' is an integer. For instance, you can have three servers, each on ports numbered 27910, 28910, 29910. Remember to set your GameSpy port numbers accordingly (e.g. 27911, 28911, 29911...)

Map Cycling
Heretic II has a new server cvar that allows you to set up map cycling.  I don't yet know what the limitations to this are.  The dedicated.cfg contains this line:

sv_maplist dmandoria,dmcanyon,dmcloud,dmhive

If you want you can just add a comma and add maps onto the list to add them to the map cycle.  I will try to see if I can figure out what the limit to the number of maps you can use in this are.

Starting the Server
Now all you have to do is either run the H2Dedicated.bat file in the root of the Heretic II directory or you could just create a shortcut that runs heretic2.exe -set dedicated.  Make sure if you create a shortcut you put the +set dedicated 1 after the quotation marks around the "c:\Program Files\Heretic II\Heretic2.exe". To simplify this I usually just install it to c:\h2\.

Now all you have to do is either run your shortcut or the batch file and the system console will pop up and your server is all ready for people to enjoy.