I worked on this a little bit more last night while watching the Rio Olympics and this is what I got so far...

nano /opt/retropie/configs/ports/quake/retroarch.cfg

input_libretro_device_p1 = 3 input_player1_a = "space" input_player1_b = "backslash" input_player1_y = "q" input_player1_x = input_player1_start = "escape" input_player1_select = "tab" input_player1_l = "a" input_player1_r = "d" input_player1_left = "left" input_player1_right = "right" input_player1_up = "w" input_player1_down = "s" input_player1_l2_btn = input_player1_r2_btn = input_player1_l3_btn = input_player1_r3_btn = # Hotkey button input_enable_hotkey_btn = "tab" # Exit emulator input_exit_emulator_btn = "x" input_exit_emulator = "del"

The hotkeys to exit the emulator do not work for me and also the Esc key doesn't show Quake's menu. Right now the only way to exit Quake is to SSH in and administer the killall retroarch command.

If anyone has any further customizations, please let me know.