Here's a couple. I'm assuming you want commands other than simple file management commands like
attrib, etc. Others can add. There's more commands often used on the server versions of Windows and the "Resource Kit Tools." Note that PowerShell is much more comprehensive in this regard.
Furthermore, given the way the Windows component architecture works, it's possible to do strange things like call functions in .DLL's to do things. A complete list of this is probably not possible unless you are terribly familiar with Windows internals.
ipconfig - display network interface IP address information
nslookup - perform DNS lookup
nbtstat - NetBIOS over TCP/IP utility
sc - commandl ine interface to control and configure services
reg - perform registry operations
netsh - perform configuration changes on network interfaces
route - display or change routing table (There's also an
ipxroute command which works if you have NWLink installed)
schtasks - command line interface to Task Scheduler.
wevtutil - command line interface to Event Viewer.
getmac - displays MAC addresses of all interfaces.
devcon - command line interface to Plug and Play subsystem - think of it as a command line Device Manager.
fsutil - filesystem-related operations
chkdsk - check filesystem on a volume
ftp - command line ftp client
format - format a volume
label - change volume label
net - performs a wide variety of "server" type operations including drve mapping, service control, user management, etc.
powercfg - configure power related settings.
regsvr32 - register/unregister DLLs