The ones I actually find myself using regularly (for the record, I use the default setup):
Middle-Click - Pause
P - Pause
F - Fast Forward (it's toggled, not held)
B - Back 1 frame
N - Forward 1 frame (you can also do this by clicking in empty space; the difference is that clicking cancels replay mode, N doesn't)
Minus - Back 1 second
< - Back 5 seconds
Space - Forwards 10 seconds
Left/Right - Directional select
R - Instant restart
U - Save replay
L - Load replay
In particular with the configuration - note that if you don't like the default frameskip durations, NeoLemmix allows you to choose your own. Durations are in frames; one second (game time) = 17 frames.