In World War I, going over the top was when soldiers crawled out of the trench and ran through no man's land while being cut down by machine guns hoping to get enough people to the enemy trench to take it, thereby gaining territory.
Now, "over the top" is an idiom that indicates excessiveness. Personally, I think that what distinguishes something that's over the top from something that's merely excessive is that being over the top is to be gleefully excessive. It's a silly excessiveness that, when applied to violence, has elements of black humor. Violent scenes in The Matrix tended to be over the top, but not the ones in Braveheart.