Unless your on an old version of windows or have installed a DOS emulator you are not running DOS programs. Alpha Centauri for example has been updated several times and includes a windows application now. Starting a program from the command line has nothing to do with whether its a windows or dos program.

Windows 7 32-bit (not 64-bit) still includes the DOS API implementation descended from the original in Windows NT.

Open up cmd.exe. Now run "edit". That's a 16-bit DOS program. You won't be able to find it in the Windows task manager - it's 'inside' ntvdm.exe.

More: run COMMAND.COM (not cmd.exe). You're now running the DOS command line, instead of cmd.exe's Win32 command line. It patches over some features, but not others, using the DOS Long File Name API. So "DIR" will list long file names, but you can't "cd \windows\serviceprofiles". You can "cd \windows\servic~1".