Depends on how your engine is tuned?!
If your engine is stock (well lightly modded) go for 36T
If you have done some extensive mods (porting and/or head polish) go for 41T.
This is purely from experience...
Before my HT would pull like a tractor, I had a huge flowing exhaust system, NON polished head and had NOT changed timing. It was pretty fun for off road!
Then came the mods. Ive polished the the head and with this mod Ive lost ALOT of torque - my theory is that the servery pitted finish in the head from casting essentially "holds" fuel in it so on the power stroke combustion takes longer. This gives you more low end torque but limits your rpm.
Then once Ive ported the engine Ive changed the timing of it and now the engine REALLY revs. Honestly its got the same pick up (little bit faster) and max revs (from sound) as a ~66cc chainsaw does now - the bike screams at top end (considering to get a better little end bearing to take this level of revs - surprisingly all my "piston ports" lightened it and has balanced the engine really well!).
Also I am running acetone in my fuel - for anyone who done this lets say that running acetone drops your torque by X amount. Well running acetone with a polished head gives you a 3X drop in torque and that's a big deal in a single speed set up.
So from now on I will not run acetone as a polished head is like permanent acetone (until carbon builds up) and gives you twice the effect of just acetone alone.
So yeah basically, 36T for stock or 40/41T for modded (when modded I mean porting, polished head - any other mods generally add torque).
For me, well I'm running a 36T and I have to get to 20Km/h before its gets on the pipe and really picks up. So with all there revs I need torque and my next mods will be an exhaust OTHER than stock (stock ATM) and a new carb (more flow/tuning), this added flow will give torque a huge boost then the expansion chamber will give the engine a bit more top end!
Sorry for the long post but I hope you can decide now over a 36 or 41T.
