Since you've already checked engine mounts, and gear shifts are fine, and the car goes smooth when the clutch is disengaged, we can consider followings:
Air in cooling system: (Any sign of leaks? Any cooling system work done lately?)
Bad IACV: (Do you get a steady idle? when was the last time you tuned/cleaned throttle?)
Uncalibrated TPS: (CEL? Do rpms start fluctuating, or go considerably high when you press clutch? Have you recently cleaned/adjusted throttle body?)