The best way to set up a Toribash server is to use command lines with the actual server. You simply point a shortcut to toribash_server.exe, and in the path, you add the command line options to the end.

The server itself is a DOS window, and doesn't accept any commands.

Detailed guide of the command line options:
-p <port> - listen port (20184)
This is simply the port of the server.
-m <frames> - match frames (120)
This is how long each match lasts.
-t <frames> - turn frames (10)
This is amount of frames that pass with each turn.
-r <sec> - reaction time (20)
How long the players have to make their moves.
-f - flags (1=DQ, 2=Decaps, 4=No Grip, 8=Fracture) (3)
See bottom, flags seem to confuse many people, so I have a detailed guide down their.
-s - sumo (0=HF, 1=HF and WA) (0)
These flags determine what is safe from DQ, hands and feet, or hands, feet, wrists and ankles.
-e <cm> - engage distance in centimeters (100)
How far apart Uke and Tori are from each other.
-j <cm> - dojo size in centimeters (0)
How large the dojo is.
-l <percent> - dismember thresh hold (100)
Self explanatory. Higher, less breaks, lower, more breaks.
-c <percent> - fracture thresh hold (0)
Same, but with fracture.
-d <model> - damage model (0=opponent, 1=both, 2=self) (0)
What can you damage?
-o <name> - mod name (classic)
What mod does the server need to use?
-C <clients> - max number of simultaneous clients (12)
Maximum number of people on the server?
-T <sec> - Socket timeout (5)
Not sure, probably how long server waits before kicking someone for no response. In seconds, I believe.
-L <file> - Name of log file
Not quite sure how this works...
-N <name> - Name of server (will show in mutliplayer server desc)
This will override the value people put in servers.txt
-D - Daemonize server
Makes the server a daemon, apparently, meaning there is no window.
-R <pass> - Remote console password
The auth password.
-P - Premium server
Makes it a regged only server.
-A <rounds> - AFK rounds. Player will be kicked if inactive this many rounds after start (3)
Self explanatory.
-M <message> - MOTD, message to display on entry.
-g <number> - Engage height.

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If the command line isn't too easy to figure out, you can use this little PHP script here: http://jok.novahost.org/suo/servertool.php
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The flags:
0=None
1=DQ
2=DM
3=DQ+DM
4=NG
5=NG+DQ
6=NG+DM
7=NG+DM+DQ
8=F
9=F+DQ
10=F+DM
11=F+DQ+DM
12=F+NG
13=F+NG+DQ
14=F+NG+DM
15=F+NG+DM+DQ

F = Fracture
DM = Dismemberment
DQ = Disqualification
NG = No grip

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For -R, it is the server auth password.
/pass <password>
Should display "Authed",
/status
Should display something like:
123 someguy 12.34.56.78 P
246 otherguy 87.65.43.21 P
To kick otherguy:
/kick 246 Some_one_word_of_reason.

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To join the server yourself:
Add 127.0.0.1:20184 "my server" to the file servers.txt and you should be able to join it.

To let others join, you must get your own ip, perhaps with:
www.whatismyip.com

Then you take that, and put it like this:
<ip>:<port> "Some server"
Remember this, preferably written down.

Then, if you use a router, forward <port> (search on how to do that), or with a firewall, open said port.

Then tell your friends the <ip>:<port> "Some server"

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Common problems:

1. You do not actually have the server running. (Dumb, I know, but I've recieved PMs about it...)
2. Make sure you are registered. (Same, people say "My server won't work" and I ask if they are even regged and they say no, dumb people...)

If you have any troubles though, please tell me, so that I can attempt to figure them out...