This tutorial was originally made by Aabra, and can be found here.

Intro

A lot of people seem to think that using IDESE or IDE is the only way to host their own server. However, this is not the case. There is an easier way for hosting your own permanent servers.

What to do

First, to keep everything neat and organized, create a new folder inside of your Skulltag server named server.
Next, right-click in this new directory and go to "New->Shortcut".
For the location, browse your to your Skulltag folder (By default it is C:\Program Files\Skulltag) and select skulltag.exe Name this shortcut SERVER 01.
Right click on your newly created shortcut and click "Properties". In "target area," it should say something like C:\Program Files\Skulltag\skulltag.exe Change it to C:\Program Files\Skulltag\skulltag.exe -host +exec "C:\Skulltag\server\CONFIG 01.txt" -file crudream.wad. Change crudream.wad to whatever wad that you plan on hosting. If you decide to use the default Skulltag maps, the -file wad.wad isn't needed.
Now we need to make our configuration file. Right-click in your server folder, and click "New->Text Document". Name this CONFIG 01
Open this newly created config file. Copy and paste the following into it.

// CONFIGURATION FILE FOR SERVERS

// Set the hostname.
sv_hostname "My Permanant Server #01"


// Set the wad url - if you set this to the exact location of the zip file
// of the wad you're using then getwad will find it.
sv_website "http://doomworld.com/crucified_dreams/crudream.zip"


// Set the banfile
sv_banfile "banlist.txt"

// Set the logfile.
logfile "C:\skulltag\server\LOG #01.txt"

// Force Skulltag to use the dmflags we want; don't set any defaults.
sv_defaultdmflags 0

// Reset the compat flags.
compatflags 0

// Make sure that we don't display launcher queries in the window.
// (Otherwise, logfiles will get HUGE!)
sv_showlauncherqueries false

// Set the skill level. 0 = I'm too young to die, 4 = Nightmare
skill 3

//*** Set the game mode. ***
//To set the various gamemodes:
//Deathmatch (current setting)
deathmatch 1
//Duel
//duel 1
//Co-op
//deathmatch 0
//Teamgame
//teamgame 1
//Team Deathmatch
//teamplay 1
//Capture the Flag
//ctf 1
//Last Man Standing
//lastmanstanding 1
//Team Last Man Standing
//teamlms 1
//Terminator
//terminator 1
//One Flag CTF
//oneflagctf 1
//Skulltag
//skulltag 1
//Invasion
//invasion 1
//Survival
//survival 1
//Possession
//possession 1
//Team Possession
//teampossession 1

//Buckshot Mode
//buckshot 1

//Instagib Mode
//instagib 1

//Call Vote (Change to true if you want to disable it)
sv_nocallvote False

//Friendly Fire (0.00 means friendly fire disabled, 1.00
//means full team damage. 0.50 is half damage etc)
teamdamage 0.00

// Set the limits.
fraglimit 25

// WINLIMIT is used for the max number of wins in a duel game
// before the map changes. 

// POINTLIMIT is used for the max number of points a team scores
// before the map changes (in modes like CTF or Domination)

// FRAGLIMIT is used for the max number of frags in either Team
// Deathmatch, regular Deathmatch, or the max frags for 1 Duel.

//TIMELIMIT is used to end the match based on the time.

// Set the maximum number of players who can participate in the game.
sv_maxplayers 8

// Set the maximum number of clients who can connect to the server.
sv_maxclients 10

//Fast Monsters
sv_fastmonsters False

//Respawn Invulnerability (Set to True to Disable)
sv_norespawninvul False

//Free Look (Set to True to Disable)
sv_nofreelook False

//Jump (Set to True to Disable)
sv_nojump False

//Makes this server a public one (Shows up on the master server.)
//Set this to False to make it private
sv_updatemaster True

//Change this setting to True if you plan on connecting to the server
//Over a local area network.
sv_broadcast False

// Set the message of the day.
sv_motd "Welcome to my server!"

// Set the RCON password.
sv_rconpassword "mypassword"

// Disallow connect/join passwords.
sv_password ""


// Set some dmflags. Should be self-explanatory.
sv_weaponstay true
sv_nomonsters true
sv_itemrespawn true
sv_noexit true
sv_doubleammo true

// Spawn drops on the floor.
compat_notossdrops true

// Set the map rotation.
addmap map01
addmap map02
addmap map03
addmap map04
addmap map05
addmap map06
addmap map07
addmap map08

8. Edit the config file to whatever you want. Change the name of the server, the RCON password, the wad url, the gamemode, fraglimit etc. This should be more or less self-explanatory. The current "example" I've setup here creates a crudream.wad deathmatch server.
9. Save the config file, then double click on your shortcut. Your server is up and running!

Advanced Server commands

Also See

SkullTag map names
Dedicated Game Server on FreeBSD - Also explains how to make a Linux server
Creating a Game Server