Bobby Shaftoe is also a central character in the World War II part of Cryptonomicon, and it seems quite likely to me that Neal Stephenson chose the name because of the nursery rhyme. He is a Marine who, after Guadalcanal, is assigned to Detachment 2702 to help prevent the German and Japanese intelligence from finding out their codes have been broken. He is the father of the character of Doug Shaftoe, with Glory Altamira. He was addicted to morphine for a large part of the book, until Enoch Root cured him. He tries to tell almost everyone he meets about a large green lizard he says he saw eat a Japanese soldier at Guadalcanal, and has frequent nightmares about.

Quote, said to General MacArthur:
"I've killed more Nips than seismic activity. I'm trained to jump out of airplanes. I speak a little Nip, I can survive in the jungle. I know Manila like the back of my hand. My wife and child are there. And I'm kinda at loose ends. Sir!"

I guess Nuage had this pegged as a nursery rhyme, which it can be - it is also used as a jump rope rhyme. But it was originally an English folk song - probably originating in Northumberland. Shaftoe is pronounced Shafty. Although there are variations in the lyrics depending on who you ask, here's a good average version:

Bobby Shaftoe's gone to sea,
Silver buckles at his knee;
He'll come back and marry me,
Bonny Bobby Shaftoe.

Chorus:
Bobby Shaftoe's bright and fair,
Combing down his yellow hair,
He's my ain for ever mair,
Bonny Bobby Shaftoe.

Bobby Shaftoe's tall and slim,
He's always dressed so neat and trim,
The lassies they all keek at him,
Bonny Bobby Shaftoe.

Chorus

Bobby Shaftoe's gett'n a bairn,
For to dandle on his airm,
On his airm and on his knee,
Bobby Shaftoe loves me.

Chorus