I'd say Freewander's personality and form suit Amy Shaftoe, but I haven't found anything that hints more closely than just their similarities.
Same goes for Thingor being Randy Waterhouse, especially when it comes to his creation of locks around the lightning bolt storage room and then learning a lot about hacking through security measures by inferring how they were bypassed.
Pluto (Pluto), Verna (Spring), Dodge (Egdod), Elmo (El), C Plus (Corvus), Sophia (Sophia), Maeve (Mab), and Bombasticus (Pan) are all spelled out in meatspace conversations.
- If I recall, Pluto is specifically called-out as the agent who's been
improving the Landform since the death of the meatspace Pluto.
- "Verna" means "spring," and when the whole REAP objection is brought
up by Z-A lawyers, they specifically say that Dodge and Verna were
the parents of the new processes.
- Dodge's identity is, of course, brought up in dozens of places.
- Same with Elmo.
- "Corvus" only appears after we read about C Plus getting ready to die
and be a bird in the afterlife, and "Corvus" (translation:
"raven/crow/jackdaw") was the name C Plus used in his Roman
- Sophia has the same name.
- Mab is identified as Maeve by Corvus and Zula when talking about the
entity that follows Adam & Eve around (specifically, I think they say
they're almost certain it's Maeve rather than 100% sure).
- Lastly, Bombasticus says she's planning to transition to the
afterlife right before Pan shows up in the story, and her music is
particularly pleasing to Egdod (so I guess that's more of a strong
hint than a totally certain indication).
When I first encountered Speaksall, I thought he might be Avi Halaby (Randy's Epiphyte business partner), who was a stellar communicator. But I can't recall Cryptonomicon saying anything about Avi being a polyglot.
Ward does sort of fit the style of Doug Shaftoe, but are we ever told if he was uploaded? I don't think he died explicitly in any previous book, but I don't think he's mentioned at all in this one.
At first, I thought Knotweave would turn out to be Maeve (what with the whole textiles/weaving angle), but that was clearly wrong. For some reason, I get the feeling we're supposed to guess who Warm Wings is, but I haven't the foggiest.
As for the others, I got nothing.
What about Captain and Honey?