Usually you can access the ingame command input for the server through double-clicking the tilde (~) key. A command line awaiting your input should appear at the bottom of your screen.
Update: As of version 171 the part below is no longer neccessary. You can now simply change the Keybinding in the Options-Menu.
Somethimes though, this doesn’t work (the command input simply doesn’t appear). In this case, the following tip might be helpful. Go to the file
At the very end of this file you will find the following lines.
ConsoleKey=None +ConsoleKeys=Tilde ;+ConsoleKeys=Tab
Replace them with this:
ConsoleKey=None +ConsoleKeys=Tilde +ConsoleKeys=Tab
(or, alternatively, in case the above fails you, with this:)
ConsoleKey=Tab +ConsoleKeys=Tilde ;+ConsoleKeys=Tab
Save the file and restart the game. You should now be able to access the Server Command Input via the TAB key.