@karda: The centre finder that Bill posted works well on irregular shapes. For shapes with "square" corners, simply use the finder to draw lines from all four corners. You will end up with a very small rectangle that you will easily be able to find the centre of. For round shapes, you use the other side of the finder and you simply rotate the finder around the piece, drawing several lines. Again, you will end up with a very small spot between the meeting point of the lines. You will easily be able to punch the centre.
As for tool handles, FWIW, I drill the hole as close to the centre as possible, but not worrying too much about being spot on. Then, I mount the handle between a steb centre in the head stock and a cone in the tail stock. The cone presses into the hole. Then, I turn the handle to the shape that I want. That way, the hole has to be in the exact centre of the final handle.