I haven't as yet had a good look at all the chain but I will do that one evening this week.
The sound is getting more frequent and I now hear it all the time in 1st and 2nd gear and sometimes in 3rd.  The one thing I have noticed, if I roll off the throttle or dip the clutch the noise stops.  Is this consistent with a stiff link or dodgy chain and sprockets?  I know the chain is turning all the time the wheels are but I'm guessing the extra load when the power is on is what causes the knocking?
I was hoping the noise would just dissappear (no such luck) because I can't really afford a chain and sprocket change at the mo, but the bike gets me to work, so if it needs doing it needs doing.
I see Griff86 says to go genuine Yamaha parts but does anyone have any other feelings on this issue?  Are there any chains/sprockets that I should definitely avoid?  What is a good price for a genuine sprocket and chain set?  the local stealer has said £170 for parts plus an hour's labour.