We've seen the green flash - no mistaking it, three people saw it, looked at each other and simultaneously said "Did you see that?".
One night, 2500 nm from the nearest land I woke the crew in the middle of the night to witness the most amazing light show in the water. Lights flashing brightly in a range of different colors, impossible to guess the depth and it went on for about an hour. It was only about a year later we discovered that it was a shoal of giant squid under the boat. Apparently that's how they communicate, they change the colour and intensity of the light continuously and flash messages to each other. Spectacular to watch.
Another thing which remains unexplained was north of Madagascar, we saw a line in the water with bright water on this side and dark water on the other side. We automatically assumed it to be a mini line squall. But then we noticed fish jumping along the line, not across it. And then a few dolphin that were obviously hunting the fish. Nothing crossed the line. But the strange thing is that the line went horizon to horizon. And even more strange, it didn't seem to be moving. We held our collective breaths as we approached it and . . . nothing. No difference in the wind, no sign of current, no change in course or heading, no change in boat-speed, no change in water temperature. We just sailed across it into the "dark" water and onwards. We looked behind and it was still there, dark on our side and bright on the other side. I did extensive research into it and still have no explanation.
Finally, another weird thing to see at sea is a full-on up-welling also called an over-fall. This happens when an underwater current is pushed up to the surface by a geological feature on the seabed. The sea surface literally boils around the boat. And the effect can be miles wide. We sailed through two of these on an Indian Ocean trip in 2004. And while you're in the confused water, the boat-speed assumes the speed of the now-surface current and it takes what feels like hours to sail through it. Bad news when it's going the wrong way which it was both times we got caught by it.