Chrono Trigger DS now seems to get past the initial Millennial Fair section in DeSmuME 0.9.2.  I've gotten a bit beyond the End of Time.

The only bug/problem I can see is that certain techs/magic won't display on the screen (example: an enemy shoots a laser, but the beam isn't drawn to the screen).

Other than that, it seems fully playable.  I'll post again if I encounter any major problems.