Windows NT and Operating Systems that were based on it (2K/XP/Vista/Seven) have their own boot loader that does not use MS-DOS, the command prompt in those systems is run under NTVDM (NT Virtual DOS Machine) and so it is not true DOS, it also suffers from many timing issues, most noticable is if you play sounds through the internal buzzer for a while as they become distorted.
On the other hand, I also doubt they will ever kill the actual command prompt as Programmers/Network Technicians will always use the command line, it is also good if you have no working GUI and gives easy access to a very simple scripting system (Batch Files).
If you ever tried to open the MSDOS.SYS file under Windows 95/98/ME (I like Windows ME

) there is an option to stop the system even loading Windows ('BootGui=0' IIRC among other cool tweaks) thus loading MS-DOS and requiring you to type WIN to load Windows manually as was the case before those Operating Systems. Interestingly the boot menu used by the Start-Up disk can be used in Config.Sys to create infinite multiple configurations which is useful for compatibility with different software if you know how to add the correct IF statements to AutoExec.bat.
EDIT: Oh, and Chips Challenge is awesome, I can confirm it is a Win16 game as it came on my first computer among a load of other cool games, most of which I have not seen elsewhere and I am unable to copy from the drive... Anybody here ever played Pipe Dream?