You may set up ConEmu as default terminal for cmd.exe, tcc.exe, powershell.exe or any other console application. In fact, you choose from what application you need to run any console application.
Also, it is possible to auto run ConEmu on cmd.exe and tcc.exe startup. Just press "Register ConEmu autorun" in Settings -> ComSpec.
More information about "Default terminal" feature
OK, inspired with question and the beginning. ConEmu build 121124 introduces experimental feature "Replace default Windows terminal".
Just turn on checkbox, point applications from you like to start console tools (for example
explorer.exe|totalcmd.exe|wdexpress.exe) and voila. You may press Win+R type
ipconfig /all and press Enter. You may even start your console application in Visual Studio debugger. New console will starts attached to the new ConEmu tab. You may also doubleclick on some executable in the Explorer window.