I have a 04 6MT, and the noise is sporadic but usually happens after driving for at least 10-20 minutes. I can hear knocking and I can also feel it with my foot lightly on the clutch, but not depressed. If I rev the engine a couple of times, the noise goes away....

Took it to the dealer, they replicate the noise....of course.

Any ideas on what it could be?

 

buying regular instead of premium gas would be my best guess as to why its happening

 

sounds like ur throwout bearing...put the clutch in..it should go away...

 

Thanks for the reply guys, but I use premium gas....

I wonder if they'll cover the throwout bearing under warranty...