Gearbox or clutch clunk, what could it be?

Hey everyone! I've been wanting to post about this issue like 3 months ago when I bought the new hatch. So anyway, this "new" hatch is an European model Civic EG4 d15b2 with S20 transmission and it has a clunk in the clutch or the tranny and It's really annoying.
There are many ways in which this sound can be reproduced: while driving in 4th, releasing the throttle and then pressing it again makes the clunk, or driving in second and releasing the throttle and then "punching" it will make the car jiggle back and forth and while the car does that, the sound is like clunk clunk, in sync with the car. The sound also occurs just when the car starts to move when putting it into reverse. The clutch seems fine, and it does not pop out of gear and it shifts fairly smooth for a 22 year old car. So, what could it be? Inner CV joints (outer ones seem ok, no clicking on turns)? Something wrong with the tranny or the clutch? Maybe it just needs oil? This is my second Civic EG and I've never heard this sound in any car that I've driven, new or old. Thanks in advance!
There are many ways in which this sound can be reproduced: while driving in 4th, releasing the throttle and then pressing it again makes the clunk, or driving in second and releasing the throttle and then "punching" it will make the car jiggle back and forth and while the car does that, the sound is like clunk clunk, in sync with the car. The sound also occurs just when the car starts to move when putting it into reverse. The clutch seems fine, and it does not pop out of gear and it shifts fairly smooth for a 22 year old car. So, what could it be? Inner CV joints (outer ones seem ok, no clicking on turns)? Something wrong with the tranny or the clutch? Maybe it just needs oil? This is my second Civic EG and I've never heard this sound in any car that I've driven, new or old. Thanks in advance!