Question: I'd like to write about the golden age of piracy and this thought came to me: is there a standard way for a 1600's ship to handle a rogue wave, or does this vary by ship design?

My inexistent degree on sailing comes from playing Assassin's Creed. In one of the games in the series, the protagonist's ship deals with rogue waves by exposing either port or starboard to the wave. Failure to do so results in the ship taking damage. However, in the very next game, a different ship must point the bow at rogue waves, taking damage otherwise. Both ships seem to be of similar shape and build, so I found the mechanics contradictory and would like to know how this goes in real life.

A general answer would be appreciated, but if different classes of ships have different modes of operation for rogue waves, an answer detailing some of those would be appreciated even more - I do expect a frigate, a galleon and a schooner to be differently affected, and would not be surprised if they should need to react differently.

Answer: 
It depends on the dimensions of your boat, and of the wave.

Basically, you do not want the wave to roll you ship, nor do you want the wave to break your ship in two.

You want to hit the wave with a part of the ship that is of length a little bit longer than the maximum trough-to-peak of the wave. This way the ship "rides" the wave, rather than being tumbled by it (too short) or ploughing through multiple waves (much too long)

With you in a **1600's ship**, facing a deep-ocean wave, the **best approach will always be straight-on**. Bow or stern matters less for the wave and more for the wind, but bow tends to be pointier and stronger, so better to hit the wave first, as the leading edge of the wave is inevitably sharper than the trailing edge.

The 1600's ship will always be out-sized by a deepsea rogue wave, so your main concern is rolling over, there is *no ways* your ship will be so long as to be in greater danger of snapping due to uneven support.
**Use catamarans**

Catamarans have some drawbacks against monohulls, but handling rough seas is one of their strengths. I don't know if it was possible to build a carrack-sized catamaran, but smaller ships would be very viable.