The one that's most frequently missed is in the Village of Sorrow. Go to the Village of Sorrow. Look for Wavebringer on your map (press the "M" key to bring up the map screen). A lot of people miss that quest because it's out of the way. Do whatever Wavebringer wants you to do.
If that isn't it, you're going to need to scour every area until you find it.
Even if the Wavebringer quest has been done, that section of the village has 3-4 Black Lotus drop sites that I used "realm-hopping" to mine. However, since Gardening was brought live, the drop rate for rare reagents seems to have been reduced significantly.
Before Gardening this section produced 2-4 Black Lotus plants per hop with a Black Pearl every 20-25 harvests. Being skunked was very rare if you restricted your hops to perfect servers.
Now, I'm lucky if I get a single Black Lotus every 3-4 hops.
I said since "Gardening" went live, but there was a "workload" balancing update very close to the Gardening update if not actually included with the Gardening update. The "balancing" update appears to be automatically moving people from server to server to improve game performance for everyone.
The result is far fewer "perfect" realms and consequently more competition for reagent drops due to the increased number of people playing on a given realm at a given time.