Try to keep your knees in natural alignment i.e. in a direct line with your hip joints, ankle joints and centre line of the foot.
When doing stuff like golf, squash, football etc. there is a lot of (unwanted) rotation around the knee joint and even some lateral/medial flexion - all of which destabilises the knee joint!!
Things like cycling can improve the damage by strengthening the ligament capsule surrounding the knee - if done with the correct alignment!!
Other movements to avoid are any which place your knees 'outside' your hips and ankles (think of cycling with your knees sticking out to the sides!!), sitting cross-legged, walking with your toes pointing outwards (instead of straight ahead), standing 'hip-shot' (all your weight on one foot and hip to one side) and sitting with your feet up and the back of the knees unsupported - all of these activities can produce unwanted stress and strain on the knee joint.
If you imagine your leg to be like two bits of wood with a metal hinge in the middle that only operates in one 'line', then consider the effects on this hinge if you continually twist it, unevenly load it etc. over a period of time - you will get uneven wear!!
The clicking that you can hear is most likely slightly loose tendons and ligaments snapping back into place as you apply pressure to them - the real worry is when your knees ache in cold weather and if you kneel down and slowly rock backwards and forwards they creak like old floor boards!! :)