I realize this is a 3 year old thread. It seems that people are describing two different noises, and both started in my Si at 6500 miles.
One noise is that "click." I only hear it when I let the clutch out (for now), and it's only one click. I'm wondering if those of you who mentioned these clicks (that sounds like a switch) years ago are still hearing it, and if it's worth going to the dealer for it.
The other is the "thunk" when shifting into 2 and sometimes into 3. Just as everyone said, it's when RPMs are too low. A/C-on makes it worse, too. I noticed that I have to give the gas pedal a little kick (push) right before clutch-in for a smooth shift. This is what's tricky, though. When driving behind someone who accelerates really slowly, RPM is too low to shift into 2nd but roaring too much to stay in 1st. Cars moving slowly don't allow me to get to the ideal RPM, and if I wait a bit to give myself room to accelerate, impatient people behind me start beeping. Hence, the "thunk."
Many newer cars with eco-mode and color lights on the dash for mpg guidance makes my Si hold back with a grunt.
:biglaugh:
Perhaps, the non-Si manual Civics do that, too. The Si is like a hyper dog that wants to sprint from the start. I love it that it's rev-happy and breathes well driven hard. I can almost feel the Si grin when it's attacking the back roads. It sure is frustrating when I can't step on the gas enough to shift smoothly as soon as I get back to civilization. I feel for people who live in heavy traffic-prone areas.