Since this thread has risen again, I figure I might as well add my version, which was cobbled together from the DT one, the Kididdles one, the Captains Courageous one, and the version Pete Coe sang at Sidmouth in 2002. I think it hangs together quite well -- my little fishie likes it, anyway, and he has very good taste:

HEY HO, LITTLE FISHIE

Come here, little fishie, and swim by my side;
And I'll sing you a song of the sea and the tide.

Chorus:

Hey ho, little fishie, don't cry, don't cry;
Hey ho, little fishie, don't cry, don't cry.

When the ship's underway and the weather is fine,
Our skipper goes aft and he's hangin' out lines. (chorus)

Then look out, little fishie, for we're after you,
But you can escape away deep in the blue. (chorus)

Little fish, don't you nibble the fisherman's bait;
Then you won't end up on the fisherman's plate. (chorus)

Just stay in your fish school and learn by the book
How not to get caught on the fisherman's hook. (chorus)

You've been swimming all day in the water so wide;
Now it's time to rest and to drift with the tide. (chorus)

The crew are asleep and the ocean's at rest
And I'm singing this song to the one I love best.

Last chorus:

Hey ho, little fishie, don't cry, don't cry;
Hey ho, little fish, you'll be whale by and by.