Here's a ride report I did when my brother and I rode around the lake in 2010.
We went clockwise. While Emerald Bay seems scary, cars are generally going slowly. The scariest part I recall was actually leading up to Emerald Bay...before it came into view. The road is fairly twisty and narrow and people are moving along quite quickly.
We started from North Shore, about 5 minutes outside of Tahoe City. We thought about driving down to south shore and getting through Emerald Bay first but decided against it due to the amount of time it would consume.