The System Menu (also known as the Wii U Menu) is a system title that provides a channel launching mechanism for users. Its title ID, 00050010-10040X00, is set in /vol/system/config/system.xml, which tells Cafe OS to launch it on boot. However, replacing this value allows something else to be booted, for example, Coldboot Haxchi.
Unlike the Wii Menu, the Wii U Menu has 3 different title IDs corresponding to each of the 3 main regions, simplifying the Update process. In addition, most OS-like functions have been moved out of the Wii U Menu, such as version.bin now holding the version, and Cafe OS handling other management.