Yesterday while I was reserving my transmission start making small clattering sound then it suddenly turn into a loud clattering sound and the car stalled out. I turn the engine back on and when I tried to shift it into reserve I can't. Can't even shift it into any gear. No matter how hard you try you can't shift it into gear with the engine on. However, with the engine off I can freely shift into all gears including reverse.

Since I can shift into gears with the engine off I decided to put it into gear first and then turn on the engine. When I do this you can hear a small on and off clunking sound. When it clunk you can feel vibration in the clutch pedal as well. When I give it some gas the noise went from clunking sound to clattering sound. Car does move, but once it start making the clattering sound I stop. After I stop the car the clattering sound continue, but fade away soon after. I let the car idle a little bit then it suddenly stalled out and fall out of first gear by itself.

What can it possibly be? Clutch, flywheel, pressure plate, clutch slave cylinder, clutch master, syncro?

 

I bet it's one of your flywheel bolts.

Only one way to find out for sure...

 

Is that the all symptom of a loose fly wheel bolt?

 

Yes the flywheel bolts could cause that. Could be a broken piece of your clutch too. Only way to know is to remove the transmission and look.

Here's someone with the same problem as you.
http://www.honda-tech.com/showthread.php?t=1593652

 

wharbone beat me too it. You can get a preliminary check by removing the inspection shield on the bottom of the transmission though before pulling completely.