Its a direct interface to the maya renderer. When you run a batch render within maya, maya itself runs 'render.exe', but keeps an eye on it, sending output to the maya console. It also has to share resources with maya itself, slowing things down slightly.
By calling it externally yourself, your saving memory that'd otherwise be used by maya, and it also allows you access to a bunch of options otherwise hidden or difficult to reach. You get a full list by typing in 'render' by itself.
Incendentally, it can be different names depending on your platform. Under windows you can use 'render' or 'mayabatch' (is that right?), under linux 'Render' (note the capital r!), and I think its the same under osx and irix.
-matt