To be honest I imagine it to be a two part OS, or one OS with a command prompt program attached, and you have to manually connect to certain things through the command prompt through passcode, but otherwise the background desktop is much like an organization owned computer: windows, wallpaper defaulted, many options disabled, like access to the c:// drive, and no internet.
I also imagine an Androidlike OS for phones or touchscreen devices (maybe embedded in control panels) with a homescreen but a custom appstore for different control panels, like the connection to doors or such.
There is probably internal servers in every site (excluding the tech site, site-15, no servers allowed) and these provide the database for all the other computers.
They probably run alot of custom applications that come down to copies of Word, Calculator, ect, things that help index. The labs will have applications that connect to lab equipment, certain places may edit A/V for use with documents, there may be scripts for things like memetic kill hazards, password locked videos, ect.