Y Snap. Hold X while in the line tool to snap all lines drawn to the X or Y axis. Shift-X will act as a toggle for the snap, allowing you to not hold the X key and still achieve the same effect.
Colour Eraser. Holding Shift and going into the eraser tool will enable you to select a colour from the swatches to erase. Only lines that are the selected colour can be erased, other lines are ignored.
Redo. Shift-Backspace will restore deleted lines. The data required to redo is not saved with tracks, so the lines that can be 'put back' won't be kept.
Easy colour playback. Hold C when pressing play, to play the track in colour.
Superzoom. Hold Shift when zooming to go in twice as far.
Scroll zoom. In any tool, scrolling with the mouse wheel will zoom in/out.
Extra stats. There are separate linecounts for each type of line, as well as a timer.