I have a manual 97 Civic EX with 225k miles all stock except air intake and exhaust. I've had this issue for a while now, when accelorating (worse in lower RPMs), where the RPMs want to climb too quickly and then come back down to match the cars speed. I just replaced master and slave clutch cylinders yesterday and my brother (last owner) replaced the clutch around 180k.

 

If the RPM is increasing but the speed is not (or not as much as it should) the clutch is slipping.