I'm in the midst of planning a short trip to Indonesia right now, and wondering if one can get from Yogya to Jakarta in, say, half a day, or in time to catch a 6.50 pm flight from the airport. Express trains that leave early enough in the morning maybe ?

that's a risk you surely can't take, take an early train from yogya and hope to be in jakarta in time to catch a flight...train travel is notoriously unreliable in indonesia, never take the time schedules for granted
whether by plane or train, don't make it a tight schedule, plenty of chances that it won't work out, this is indonesia after all...

This should be the Indonesian railway site, though it is now reponding right now.
http://www.infoka.kereta-api.com/</a><BR>Maybe it will work for you.

It is working now.
The Jakarta stations are shown as Jakartakota (old part of Jakarta, in the north, a bit closer to the airport) and Gambir (ir does not say Jakarta-Gambir) in the central area.
The only suitable trains are overnight (arriving around 6am) or this one:
Depart: 08.53 (Yogyakarta) Arrive: 15.57 (Gambir)
This one does not seem to go to Kota.
At that time of day rush hour is starting. From Gambir to the highway is not so easy, so by taxi it would take at least an hour, mabe 90 minutes - or more if you are unlucky, if it is raining etc.
That makes it very tight for your flight, though not impossible.
I probably would not risk it.
I don't know how accurate that timetable is.

the time table is a guidance, but watch out for enourmous delays:
a while ago I took the night train (business class) from surabaya, leaving in the evening and supposedly arriving in jakarta the next morning, a 12 hour trip, I had a flight to catch in jakarta at 4 pm, plenty of time you would think, well I nearly missed that flight, the train came in about 1 pm (a 7 hour delay!), and I had to rush to the airport, with the traffic jams in jakarta and all
so now I always make sure I arrive in jakarta a day ahead of time, I just don't risk it anymore, too much stress, and who needs that?
anyways an extra night in jakarta is good fun, it's a real party-town!
sometimes the train, even the expensive ones (argos), broke down because accident etc
like the #6 said, dont rely on the timetable too much