Graphics is an obvious subcategory which most of the existing commands in the wiki should belong to. But it's also a command itself. How should that work?
'Graphics' is both a category and an article. Goto 'index.php/Graphics' for the function, and 'index.php/Category:Graphics' for the category that should contain all the graphics commands. If want to, you can start adding all the graphics-related stuff into that category. The Wiki treats both path separately, so there's no problems doing that.
Also, Todd, I see there are some modules mentioned now, but only the Audio one has the (Module) suffix. They are all meant to have this, right?
No, I wanted to keep the names as simple as possible, because it looks nicer to see "AudioSample", than to see "AudioSample (BRL Module)" everywhere. The Audio module is named "Audio (Module)" only because the name "Audio" can interfere with another Audio category (one which should contain articles relating to creating and playback of audio, rather than a list of functions for the module).
And finally, I have my A* module that I've been documenting lately so this is a prim candidate for the Wiki, but how do I get the module file up there for people to download and use?
You should first create a category for the module, by typing "index.php/Category:MyAStarModule" (or whatever you've called it), and add short description to that page, and place it in 'User Modules' (add the line '[[Category:User Modules]]' to the end of the page's text. Then, add a page for each function, and add it to your module's category ('[[Category:MyAStarModule]]'). You should just name the pages the same thing you name the functions. Unless you think that it could interfere with another article later on, you don't even need a suffix, etc. If you decide you do, just use your module's name (e.g. "AStarFunction (MyAStarModule)"). As for upload a zip file containing the module, I'm getting uploads enabled, so you can just upload it and place a link on your module's category page.