Non Temporary Duty:
Not counting the captains...
Nor mirror universe
Sulu is shown in the movies to captain an Excelsior class.
Spock is captain of record when the Enterprise is a training ship (ST II)
Riker moves on to the Titan in Nemesis.
Dr. Crusher gets the Pasteur (All Good Things)
LaForge has command of the Challenger in 2290 (Timeless)†
Colonel Kira takes over DS9 when Captain Sisko "disappears."
None. We don't see any future bits for these characters, and all commands are temporary duty, not "permanent party assignments".
† Included because the time-loop has to occur in order to exist. It's not an alternate timeline; it's a temporal anomaly.