I have always used good old Permatex #2 on the intake bolts. As did the factory. A couple turns of Teflon tape would probably be OK but don't over do it. If you make the tape too thick, the bolts will most likely reach their torque value before providing the desired clamping load. Teflon tape is really designed for tapered (NPT) threads. The reason for sealing the bolt threads is to prevent oil from traveling up the threads and pooling around the bolt heads. The intake bolt holes are drilled through into the lifter valley. I always use a hardened flat washer under my intake bolts as well, with a little sealant on the back face of course.
As for the ends of the lifter valley, I personally always use RTV (and it is one of the few places I do use that nasty stuff). Heres why. If you have surfaced your heads and not cut enough off the intake faces the manifold will sit high relative to the block and the OEM style cork/rubber end seals may not be tall enough. If the block has been decked, or the heads cut and the correct amount of material faced from the the intake side of the heads, the manifold will now sit lower relative to the block and the OEM seals will possibly prevent the ports from sealing well. RTV will cure to the exact size needed to seal. Make sure the surfaces are super clean (Acetone as a final prep) before applying the RTV, and follow the manufacturers instructions exactly.
Now, if you are one of those misguided souls who runs an unpainted aluminum intake, masking tape will be your friend. Mask the ends of your intake, and about 1/8" down from the edge of the block. This way you can smooth the RTV with your finger, just like caulking. In fact you ARE caulking the intake with RTV. Then, after waiting about 20 minutes peel the masking tape and you will have a nice clean line.
