As current keyboard layouts and the WiiMote, Nunchuck and classic controller buttons are different from the keys and buttons of the MSX, some keys have a different function than they used to have.

As far as it is possible, all keys will be the same.
There are some differences:
F6-F10: current keyboards have F1-F12, the MSX only has F1-F5, F6-F10 map to the buttons that are on the same place, which are: Select, Stop, Clr home, Insert and Delete.
F11 is mapped to quick-change disk (an emulator feature).
F12 is mapped to the 'home' button of the controller to make the GUI fully controllable using the USB keyboard.

WiiMote buttons A and 2 are mapped to MSX button 1
WiiMote buttons B and 1 are mapped to MSX button 2
The nunchuck button Z maps to button A (of the WiiMote)
The nunchuck button C maps to button B (of the WiiMote)

It is possible to make a custom keymapping for each game.
This is done in the gamelist.xml files, which can be found in the /MSX/Games folders
by supplying a <KeyMap> element.

Supplying the <KeyMap KeyboardJoystick="true"/> will result in the following mapping:
WiiMote 1 will map to keyboard:
Button A and 2 to space
Button B and 1 will be unmapped
The direction arrows go to the corresponding directions on the keyboard

WiiMote 2 will map to joystick 1
Button A and 2 to MSX Button 1
Button B and 1 to MSX Button 2
The direction arrows go to the corresponding directions of joystick 1

It is possible to make a different keymapping for each key.
A custom keymapping example:
<KeyMap buttonA1="space" button11="left" button21="right"/>

List of names/values for the buttons (these are the values BEFORE the '=')

WiiMote 1 buttons:
"up1"
"down1"
"left1"
"right1"
"buttonA1"
"buttonB1"
"button11"
"button21"
"home1"
"plus1"
"minus1"
Classic controller 1 buttons:
"buttonX1"
"buttonY1"
"buttonL1"
"buttonR1"
"buttonZL1"
"buttonZR1"

WiiMote 2 buttons:
"up2"
"down2"
"left2"
"right2"
"buttonA2"
"buttonB2"
"button12"
"button22"
"home2"
"plus2"
"minus2"
Classic controller 2 buttons:
"buttonX2"
"buttonY2"
"buttonL2"
"buttonR2"
"buttonZL2"
"buttonZR2"

USB keyboard keys:

NOTE: Since revision r123 (not release V1.0) the names of the numbers, keypad buttons and symbols are changed, the old names are not described in this guide anymore, because they are unusable in V1.0!

direction: "up", "down", "left", "right"
letters (must be lowercase): "a" - "z"
Numbers: "key_0" - "key_9"
Keypad buttons (are in brackets): "num_0" - "num_9", "num_period", "num_slash",  "num_asterisk", "num_minus", "num_plus", except for "num_enter" and "num_equals"
Function keys (also lowercase): "f1" - "f12"
Symbols: "exclamation", "doublequote", "hash", "dollar", "percent", "ampersand", "quote", "open_parenthesis", "close_parenthesis", "asterisk", "plus", "comma", "minus", "period", "slash", "colon", "semicolon", "less", "equal", "greater", "question", "at", "open_bracket", "backslash", "close_bracket", "caret", "underscore", "backquote", "open_brace", "vertical_bar", "close_brace", "tilde"
Other characters: "space", "return", "backspace", "tab", "escape", "insert", "delete", "home", "end", "page_up", "page_down"

List of actions to which the keys can be mapped (quoted values AFTER the '=')

MSX Joystick 1 buttons:
"joy1-up"
"joy1-down"
"joy1-left"
"joy1-right"
"joy1-button1"
"joy1-button2"
"joy1-button3"
"joy1-button4"
"joy1-button5"
"joy1-button6"

MSX Joystick 2 buttons:
"joy2-up"
"joy2-down"
"joy2-left"
"joy2-right"
"joy2-button1"
"joy2-button2"
"joy2-button3"
"joy2-button4"
"joy2-button5"
"joy2-button6"

MSX Keyboard keys:

Direction keys: "up", "down", "left", "right"
Letters (should be lowercase): "a" - "z"
Nnumbers: "0" - "9"
Keypad: "num0" - "num9", "numperiod", "numdiv", "nummul", "numsub", "numadd" and "numcomma"
Function keys (also lowercase): "f1" - "f5"
Special keys: "stop", "cls", "select", "ins", "del"
Symbols: "neg", "circomflex", "backslash", "at", "leftbracket", "semicolon", "colon", "rightbracket", "comma", "period", "div", "underscore", "graph", "torikeshi", "space", "jikkou"
Other keys: "esc", "backspace", "tab", "return", "ctrl", "leftshift", "rightshift", "caps", "code", "pause", "print"

ColecoVision keys: "coleco1-0", "coleco1-1", "coleco1-2", "coleco1-3", "coleco1-4", "coleco1-5", "coleco1-6", "coleco1-7", "coleco1-8", "coleco1-9", "coleco1-star", "coleco1-hashmark", "coleco2-0", "coleco2-1", "coleco2-2", "coleco2-3", "coleco2-4", "coleco2-5", "coleco2-6", "coleco2-7", "coleco2-8", "coleco2-9", "coleco2-star", "coleco2-hashmark"

Hotkey functions:
"hotkey_quit"
"hotkey_fdc_timing"
"hotkey_sprite_enable"
"hotkey_msx_audio_switch"
"hotkey_front_switch"
"hotkey_pause_switch"
"hotkey_wave_capture"
"hotkey_screen_capture"
"hotkey_load_state"
"hotkey_save_state"
"hotkey_card_remove_1"
"hotkey_card_remove_2"
"hotkey_card_auto_reset"
"hotkey_disk_change"
"hotkey_disk_remove_a"
"hotkey_disk_remove_b"
"hotkey_disk_auto_reset"
"hotkey_cas_rewind"
"hotkey_cas_remove"
"hotkey_cas_read_only"
"hotkey_cas_auto_rewind"
"hotkey_cas_save"
"hotkey_emu_pause"
"hotkey_emu_stop"
"hotkey_emu_speed_normal"
"hotkey_emu_speed_increase"
"hotkey_emu_speed_decrease"
"hotkey_emu_max_speed"
"hotkey_emu_reset_soft"
"hotkey_emu_reset_hard"
"hotkey_emu_reset_clean"
"hotkey_volume_increase"
"hotkey_volume_decrease"
"hotkey_mute"
"hotkey_stereo"
"hotkey_window_size_normal"
"hotkey_window_size_fullscreen"
"hotkey_fullscreen_toggle"