regedit.exe
~/HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/KeyboardLayout/
Scancode Mapという名のバイナリ値を作成、編集
CapsとCtrlを入れ替えたい場合
00 00 00 00 00 00 00 00 03 00 00 00 1d 00 3a 00 3a 00 1d 00 00 00 00 00
両方共Ctrlにしたい場合(Capsをなくす)
00 00 00 00 00 00 00 00 02 00 00 00 1D 00 3A 00 00 00 00 00 00 00 00 00
より汎用的な方法として、SharpKeysを使うと簡単で良い。
http://www.howtogeek.com/howto/windows-vista/map-any-key-to-any-key-on-windows-xp-vista/