Run windows command in background
Unfortunately I do not think that this is possible.
You can do this in a Windows Scripting Host script, with something like:
Set oShell = WScript.CreateObject("WScript.Shell")
Set oProc = oShell.Run "<your command here>",0,True
Where the "0" states that the resulting window should be hidden (for other options, see the documentation at http://msdn.microsoft.com/en-us/library/d5fk67ky(VS.85).aspx) and the "true" states that you want to wait for the command to complete before your script carries on.
It would be a simple exercise to wrap this up in a generic "run this command hidden" script that you could use from the command line.
If you have Microsoft's PowerShell installed, then there may be an easier way to do this (I've not worked with PowerShell yet).
If you are happy to have the window minimised then you can do that with the "start" command that other mention. Unfortunately the "/B" option (which sounds like it is what you want) is only for commands and it doesn't stop windowed applications appearing on screen.
Note: which ever of the above you use to you start a program with a hidden/minimised main window, there is nothing to stop it creating new windows that are visible, or bringing the main window up and into focus, once it is running.