I've been on two cruises that had significant seas...
2005 Hurricane Wilma, we were on
RCCL and we actually sailed through part of the hurricane -- 35 foot waves. We made the best of it. Unfortunately we probably got into a little more that most cruise ships will, but our ship had been tapped to go to Yucatan Peninsula to help with the relief efforts there so our Captain made the choice to get the ship back to Florida ASAP so that they could go there. Unfortunately, when we got to Florida - all the ports were closed - Ft. Lauderdale, Miami, etc due to damage to those cities from the hurricane. So, we sat off the coast of Florida for almost 2 days waiting to get clearance to dock. It was crazy and a lot of people complained. My DH and I got some fun video of the storm and some really nice photos of extremely calm seas the day after.
2010 - Magic in the Mediterranean. We were on the first
DCL Med. cruise in April 2010. We were on our final day at sea and were hit by a really freak storm. I think they said we had close to hurricane force winds and I heard anywhere from 25 - 35 foot seas? The ship was actually listing on this one. Really crazy -- my boys got ill - but some Dramamine, a couple of nice cozy spots in Deck 2's portholes and some sleep and they did fine

The Captain did a fantastic job trying to get us out of the storm as quickly as possible. By evening all was good and we had a really nice final night on board. Was it a bummer that it happened - sure. Did it ruin our trip? Absolutely not. If anything, it gave us some great pictures and a wild story to share.