The VGUI that has been in Half-Life since version 1.1 allows a much greater flexibility in the kind of information that you can provide your players with. Consider, for example, the class information that TFC and Day of Defeat provide you with when you are selecting a class. Putting it in the documentation is nice, but it helps to be able to go over things while in the game. Sure, you can get along without it, but it drastically reduces the learning curve of the game if you can get class info at a glance without even closing Half-Life. Even without utilizing the vgui, consider at least what the game menus can be used for.
Some mods have things like map switching commands or bot controls in the menus now.
It helps enormously when you're running a listen server, believe me. A solid manual is invaluable. Any commands that aren't in the control setup should also be listed, as well as any miscellaneous features. The purpose of this is two-fold. Firstly, mods are getting bigger by the day, and the decision of whether or not to download a mod is often settled in some people's minds by a glance at the documentation on the site.