Can you tell if it is coming from the clutch pedal itself (inside the car) or is the noise coming from outside the cabin (under hood or under car). I've had two older Hondas with squeaky clutch pedals. One car was a cable operated clutch and the other hydraulic, both turned out to be the return spring sheaths on the pedals themselves.

My dealer lubrictaed the slave cylinder and the squeak is gone. At least that is what they said they did.

I have the same problem and the dealer tried to fix it 3 times. The dealer lubed the slave cylinder first, but it didn't work, so they told me to come a week later and they will replace the whole pedal assembly. When they replaced the clutch pedal, the squeek was gone for 1000 miles and returned with a louder squeek. The service manager had it lubed again, but the problem still existed and he told me he doesn't know what to do anymore. The service manager then told me that a TSB might come out on a new clutch pedal, but he also told me not keep my hopes up because he was just speculating since so many people have this problem. **To note: My service manager had a RX8 with the same squeek problem so he was real helpful and he couldn't get it fixed either.

Buy a can of ATE Super Blue, take it to your service manager and tell him to replace the fluid in the clutch hydraulic system. This took care of that same problem on my RX-7. It may not work on your car, but it won't cost you much to try.

The squeeky pedal is just because you need lube on the spring.. Just stick yer head under there, find your clutch and follow it up. Get a can of silicone lube and give it a quick spray. Ive been squeek free for 25k miles now..Dont use WD40, it attracts dust.

I had the same problem after about 500 miles on my '06 GT. The dealer replaced the clutch pedal assembly and the problem has not come back.
I had my clutch pedal replaced last week for a squeak. The squeak is gone and the clutch works nicely, although I noticed that it has to be held right against the floor for the car to crank. I never noticed this before, although I've only had the car for a month.

How high off the floor can you hold your clutch pedal before the starter interlock won't allow the car to crank? There are 4 possible sources of noise that I found,the pedal pivots,the clutch cylinder,and 2 switches---in my case a push rod on the lower switch was making the noise and some silicone grease quieted it.
You have to get right into the footwell and identify the source for your car.
I crawled ainto the footwell with my troublelight and relocated some of the silicone grease that they liberally applied to my clutch pedal assembly onto the switches and clutch cylinder and the squeak is gone (at least for now!).