I've purposely avoided the speculation train as much as possible, but I don't think we're ever going to know a concrete answer in this case.
- Based off the things we know, transponders don't turn themselves off. If the radar return over Pulau Perak does indeed turn out to be the missing 777, it didn't end up flying that route on accident.
- A complete electrical failure just doesn't happen either. Not saying that it isn't possible, but there are so many redundant backups on a 777 - all the way down to a ram air turbine - it just makes it highly unlikely. Even if it was a catastrophic electrical failure, the engines would still spin, and the ram air turbine would provide hydraulic pressure to the control surfaces. The pilot then could have kept flying using the magnetic compass until he was over land and able to locate a suitable airport to land at. He had plenty of fuel to find somewhere.
- Uncontrolled decompression ala Payne Stewart is another theory, but this aircraft was over-water and flying on a programmed FMS. It would have kept flying the route until the FMS was out of instructions.
- Hijack is yet another theory, but it would have to be almost surgical to have absolutely no indication from either the front or back of the aircraft. There are sat phones at crew stations. The hijackers would have to have a very advanced knowledge of the systems on a 777, and flying in general, to be able to disable any and all reporting systems and weave it around ground radar range.
- In-flight breakup seems unlikely because debris would have likely been spotted by now in the Gulf of Thailand. Plenty of stuff on aircraft float. The water currents and unremarkable weather recently would have aided in the recovery.
- Insert any number of broad government conspiracy theories...
Personally, I think someone intentionally took this aircraft hours over the Indian Ocean until the fuel ran out. Pilot suicide is something awful to think about, but I just don't see any other way an airliner like a 777 just goes completely off the reservation like that without someone that knows what they're doing. Radar coverage in that part of the world is shoddy at best, so it wouldn't be hard to go poof in the night at the hands of someone that's familiar with where the coverage gaps are. Pull the right circuit breakers, decompress the cabin so everyone is unconscious, and head for nowhere. Even that sounds awfully wild, and nearly impossible with automated backups in place, though.
One thing I am sure of: the Malaysian government seems completely inept at manning an aviation investigation. The number of releases and retractions they're making aren't making the search any easier. They seem to have no clue about what they're doing. NTSB should be running this investigation, but that would require the full and unmitigated cooperation of the Malaysian, Thai, and possibly Vietnamese governments. I'm not saying it's impossible, but that would indicate the white flag being raised in front of the world.