Okay, there are many programs - all have their positive and negative points!
The 1.1 patch (by microsoft) - this should be applied as 'standard' to the server (personally thinking).
Ioncross Server Operator - you can ban accounts, edit, change settings, filter what people can and cannot use (by 'hash' codes) etc.
FLCD (Freelancer Cheat Detection) - this program means players have to use a client to connect to the server, and it scans their files. Supposed to be the *best* one around, but causes lag and other problems apparently.
There was another one, but I cannot remember what its called. For Ioncross
www.ioncross.com, for FLCD, ask after it
here - you will need to register and look for a guy called Niwo.
The MS 1.1 patch is stickied in the server forum.