What is that engine noise ?
YouTube - subaru engine noise

 

is your car a 97-99 (or there abouts ) uk turbo 2000 ?? if so its possibly piston slap.. thats what it sounds like to me...and if so its just that the pistons have some lateral movement in the barrel....not an issue as far as i have been led to believe from peeps in the know and quite common....

 

My car is '00 Legacy 2.5 N/A.

 

sounds like some sort of bearing noise.
check bearings of the dynamo and AC pump.
you can do this by placing a large screwdriver against suspected bearing and put your ear on the back of the screwdriver (kind of like a stethoscoop).

 

I ran the engine without v-belts and it was also knocking.
Since this goes away complitly after engine is warmed (but is back very quick, some of it can be heard just after engine is not running for 10 minutes). I think this is either a piston slap or a timing belt tensioner issue. I tried to locate this noise using ski sticks (rubber end to ear) but I cant.
Some more tips:
1. My engine does not burn oil. I cant notice any oil loss during last >12000km. Is it posible that a piston slapping engine does not take oil at all ?
2. Knocking is not audiable at idle. Only audiable when raving engine / accelerating, best audiable at 1500-2000rpm. If I hit a throtle quickly and then let go quickly it makes a single knock.
3. I'm running mobil 1 5W30 oil.

 

Can you locate it better? Listen using a long screw driver as suggested above to the center of the engine and over each cylinder head. It sounds like it could be something in the heads i.e.tappets... I would also suggest you run thicker oil (10w40 - 15w50) although I dont know what oil your meant to run in a 2.5na but thicker oil is better in the 2.0turbo engines.

 

sounds like bottom end to me
Could be wrong though

 

best way to tell if you have a failing bottom end (con rod bearings) is to do exactly as you did revving the engine and lissen for the knock and then pull the plug of the spark plugs one at the time.
If the knocking disappears you know which cilinder has a busted bearing.

 

Is it posible for a con rod bearing to stop knocking when engine warmes up ?