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top end is usually associated with the cylinder heads and valve train (maybe intake and fuel system, depending on who your talking to). bottom end is your rotating assembly (crank,rods,pistons) and block.
Secondly, top end can refer to two things... Top end as in the top end of the motor (as previously described), or top end, as in the top end of your rpm range. If you are looking for parts to help your top end, as in performance, you will look to items that will increase the limit of your rpm range or maximize it's performance once there.