Yamaha DT3.  Looking at the service manual I only see yamabond applied on the side cover gaskets and the case if you split it. I'm wondering if it is best practice to put some sealer on any of these gaskets? 
float chamber, valve seats, cylinder base, manifold intake (the thick one), manifold ( the thin one)>

I think the Yamabond is for a case where you aren't taking it apart for maintenance and such... Like a glue, if you will..
Sneezles61

Yeah, I was just wondering about using something like permatex high tack  gasket sealant on any of those gaskets.

a seasoned journeyman I worked with when I was a diesel apprentice in a past life used to tell me to coat all my gaskets with a thin layer of oil before installing so parts would be come apart easily down the road and gaskets could potentially be reused again. I realize this is counter to the discussion posed here. I probably wouldn't do that on the center case gasket but I have applied this on the clutch covers since they sometimes need to be removed occasionally for different reasons. 

the where to use sealer is a very good question.
I am not an expert, but have much experience over the last 40 years making mistakes, my approach on these old bikes has been to use Yamabond on case halves as specified, but also a very light smear on cylinder base gasket too.  I have also used on the intake of my DT360 where I was resonably sure that the raised rubber bead would be unreliable...here I chose to use a gasket on each side, each with a very light coat of yamahabond.  I never use any type of sealer on carbs or anywhere in the fuel system, the exception being some epoxy to plug a small seam leak on tank.  Lastly, I avoid RTV whenever possible because IMO in creates more issues that it solves.  The only exception is that sometimes I will use hi temp RTV when all other options fail

The simple answer is no. Yamabond 4 for center cases, all others dry with good quality gaskets. Just make sure your mating surfaces are clean and flat. I've been doing this for years with no issues. 
However if you want to put a very light film of yamabond on other case gaskets it wouldn't do any harm especially if you see damage mating surfaces.  Never put anything on a carburetor float bowl gasket except a new gasket. Again, if you make sure your surfaces are flat and clean and don't over tighten bolts and screws you should be good to go.

I just glue the center cases as have no gasket, & grease the rest for easy removal as mine seem to be apart regularly.