Here's my contribution.
Belthasar
Last seen in Terra Tower in 1020 AD, Another Dimension. His whereabouts in the unified timeline are unknown. He is probably playing Poker with the Entity.
Dalton
Last seen passing through his golem summoning portal in 12,000 BC. Presumably he died, but he may also have appeared in another time-period or dimension. His current whereabouts are unknown.
Doan
Last seen departing in a Time-Gate at the Moonlight Parade in 1000 AD. This version of Doan may actually be from the new timeline. Doan is probably the dome supervisor in 2300 AD.
Gato
Last seen Lucca's house, 1015 AD, Another dimension. Gato was destroyed in a house fire during the events of Chrono Cross. Gato's status, or whether Lucca's house was even destroyed in the unified timeline is unknown.
My belief is that Lucca's orphanage was not destroyed in the new timeline and Gato should be intact.
Gaspar
Last seen in the End of Time. His location should be protected from any time-line changes. Gaspar may have stayed in the End of Time for the remainder of his life or travelled to another location. His current whereabouts are unknown.
Johnny
Last seen in the Dead Sea, 1020 AD, Home dimension as wreakage. The Dead Sea was destroyed by FATE during the events of Chrono Cross. Johnny's status in Another dimension is unknown. Johnny's status or the existence of the Dead Sea in the unified time-line are unknown.
My belief is that Chronopolis would not be warped to the past in the unified time-line so Johnny should still be in 2400 AD.
Melchior
Last seen during the Moonlight Parade in 1000 AD. Presumably, he lived out the rest of his life in that time-period.
Mother Brain
Mother Brain was last seen 2300 AD in the desolate future, and was destroyed by the time travellers. In the new future, Mother Brain's design was incorporated into FATE in Chronopolis. The status of the actual Mother Brain computer in the new timeline is unknown, she might still be coordinating the Robot Factory in 2400 AD.
Schala
Last seen in the DBT during the conclusion of Chrono Cross. Presumably Schala is searching through time and dimensions for Serge and/or Magus. Where Schala ended up during the ending sequence is anybody's guess.
Toma
Toma the 1st died in 600 AD in the Dragon's Claw.
Toma the 13th was last seen in 1000 AD, and probably lived out the rest of his life there.
Toma the 14th was last seen exploring the El Nido in Another dimension (or taking up gardening in Home dimension). He probably explored El Nido in the unified time-line.
Ayla
Last seen in 65 million BC and most likely lived out the rest of her life there.
Frog
Last seen in 600 AD and most likely lived out the rest of his life there.
The Masamune
The Masamune was last seen in the DBT during the conclusion of Chrono Cross (as the Mastermune). Serge probably didn't keep it when he returned to 1020 AD, since he lost his memories. The status of the Masamune, Mastermune or Masa, Mune and Doreen in the unified time-line are unknown.
Robo
Robo was last seen in 2300 AD. Somehow, Robo was incorporated into FATE as the Prometheus Lock in 2400 AD, and was later deleted in Chronopolis in 1020 AD, Another dimension. Robo's status in Home dimension is unknown. Robo's status or the existence of Chronopolis or FATE in the unified time-line is unknown.
My belief is that FATE was not constructed in the unified time-line, so Robo should still be intact in 2400 AD.
Lucca
Lucca was last seen at the Moonlight Parade in 1000 AD. In 1015 AD, Another dimension she was captured by Lynx and Harle to disable the Prometheus Lock and was supposedly killed. Lucca's status or whether or not she was captured in the unified time-line is unknown.
My belief is that Lucca was not captured in the unified time-line and would presumably live out the rest of her life in that time-period.
If Lucca was involved in Belthasar's plans, either the orphanage scenario was not as it seemed, or Belthasar rather callously orchestrated her capture and possible death. I find the whole situation suspicious.
Crono and Marle
Crono and Marle were last seen at the Moonlight Parade in 1000 AD. It is implied in Lucca's letter that they were still alive as of 1015 AD. Their status in the unified time-line is unknown.
My belief is that Crono and Marle lived quietly in what was left of Guardia.
The Ghost Children
The Ghost Children are reflections of a lost timeline (or whatever). Presumably, they would no longer exist in the unified time-line.
Magus
Last seen in 12,000 BC. It was implied in Lucca's letter that he may be time travelling in search of Schala/Kid. His current whereabouts are unknown.