My pads are new but whenever i apply the Brakes on my 2000 VW Passat i hear a Clunking sound in the front left Tire area any idea what it is?

Understand that when you apply the brakes you're putting tremendous torque on the hub assembly. If the lower control arm bushings or the strut bushings are worn, you could certainly get the kind of noise you're describing. If the brakes weren't put in properly you could also get that noise, but it's not likely since brakes cannot usually be installed improperly.