It seems I may have the same problem as you too! (Quick stats: 2002 Accord Coupe, F23A1 w/ 5spd, only 120,000Kms!) I've started noticing this very faint knocking sound about 8 months ago, it seems it would come and go. I even went to show my mechanic buddy about a month ago, but I couldn't get it to do it. Well, about two weeks ago I noticed that annoying "helicopter/knocking" sound linger a bit longer than normal, even when I drove the car for an extended period of time or when I revved it around the 2000 rpm range (±300) when in neutral, the knocking was still there. I tried to isolate the noise using a mechanic's stethoscope and I placed it all over the engine, but from the top I could not hear the sound as definitive as I wanted it to be. Well, the next day after work, I took it to the dealer and I had one of their senior mechanics diagnose the knocking noise I was talking about. We had to drive it around for a bit, to get the car warmed up good, as my work was close by. He was able to finally locate the sound when he had the car up on the hoist and one of the other mechanics was revving the engine to the 2000 rpm mark (±300). The sound was coming from the bottom end (you could hear it big time compared to when listening from the top), he said it was most likely the thrust bearing for the crankshaft, as the car is a 5spd. That explains why the sound still lingered when the plugs were pulled one at a time, thinking it was rod knock. He said this is somewhat common and not to worry. I ended up draining the oil yesterday (even though there was about 3000kms left before the next change), there was nothing noticeable when I strained it, the magnetic plug showed nothing, I even stuck a wire in the oil pan hoping to pull something, but nothing came out, just clear oil! I still think I may end up removing the oil pan just to be sure that it may not be something loose like the windage tray or some bracket of some sort. It's funny because I was talking to the service adviser the day I had the mechanic check it out, and we started talking about that maybe I should just sell it and buy a newer Accord. I laughed and then said, that I was going to but apparently the 4 bangers have some defect where they burn oil like crazy! It was the K24 engine, the same engine in the TSX (04-08), I know I'm kind of off topic, but my point is, it really doesn't matter what you get, there's always going to be something.
PS. Anybody know if you can remove the F23A1 engine from the top of the 6Gen Accord with an engine hoist? Just wondering! Thanks