I replace my front brakes because while driving i heard a metal to metal rubbing sound, and i did need brakes, So once done with the brake job, i top off all my fluids, while car still on jacks i decided to shift it into gear, that sound was still there, my cars is lowered and trans was rebuild about 40.000 miles ago.
i never have replace the axles, so hopefully its just the axles. cause to get that tranny fixed was a pain. that sound seems to come from the left(D) hand axle input housing

 

http://s47.photobucket.com/albums/f1...1006091737.flv

could be the axle but from your description and the video, I can't be sure. Is the noise coming from inside the trans? Does it look like the axle popped out of the trans? Are the boots torn/ripped?

 

the boots are not torn, as for a popped out axle, i see it in there, but first time dealing with this issue, i used have a civic with this same deal but i wrecked it before dealing with it, the car shifts and goes, i probably need to inspect it more.
Would i be able to take out the axle and put it in gear?

But the sound comes from the rear area

 

theres a metal ring on the axle that should be right against the axle case. You can get under the car and see if it's sitting against the case or not.
Yes, you can shift the trans with no axles...

 

i think the problem is that the bearing to the gears in your differential went bad. which makes a knocking noise just like the noise i heard in the video. not 100% sure but its worth checking....good luck!

 

Well i was going to take the axle out today, But i dont have the axle nut socket
But while i took the caliper and rotor out, i put in gear and did the mechanic trick with a giant screwdriver to hear where the knocking is coming from, and i think its my Hub assembly bearing, my whole strut tower vibrates Hopefully im right and not that the sound travels from the axle,

 

Is the car leaking transmission fluid??

 

Almost sounds like when I broke a joint after extensive wheel hop...only difference is the car wouldn't move after that