A: Toggle automatically advancing the dialogue
R: View the chat log
Ctrl: Hold to skip through dialogue
Z: Open the save window while not in battle
X: Open the load window while not in battle
Arrow Keys: Cycle through the movement squares and menu options
Enter/Space: Confirm your selection (after selecting using the arrow keys), Advance the dialogue
Esc: Close the open window

A: Use an item in battle
S: Escape from battle
Z: Attack
X: Defensive stance
X or →: Defend an enemy attack
Z or ←: Counterattack after defending an enemy attack
V: Use the Identify skill. Afterwards, 'Z' opens the spirit index and 'X' allows for keyboard input
B: Use the Capture skill
N: Use a Yin skill
M: Use a Yang skill

Sources: Trial and error
Icon Source: http://en.icône.com/tag-keyboard-0