Noises when using or engaging the clutch often mean that there is a problem with the clutch or its linkages. If you depress the clutch and hear a noise, it's likely it has something to do with the clutch itself and not the transmission.
One more thing to note on clutch noises: It's important to figure out if the noise is coming from the clutch pedal area or the transmission. If you hear a noise coming from the clutch pedal, try sticking your head up under the dash to see if you can pinpoint where it's coming from. Noises often come from the clutch pedal return springs or sometimes the clutch linkage itself. I've even seen clutch pedal mounts break and cause noises and issues when activating the clutch.
As for noises at the transmission, look to the clutch linkage itself. Some clutch linkage is adjustable and you might be able to fix the problem with a simple adjustment. Here's the procedure for adjusting a cable-operated clutch on a Honda. It's a similar process for other makes.
Sometimes the linkage gets rusted or bent. If that's the case, try a little lubrication to see if that cures the noise or changes it enough to confirm your suspicions. If you have a high-performance clutch, expect problems with the clutch linkage or hydraulics. High-performance clutches have a much higher clamping force, and as a result they put a lot more strain on your clutch linkage. If you have a high-performance clutch and you’re hearing noises, be sure to check the clutch and its linkage.