I have the same problem with the base of my basil. Im not sure what it is either, and im a little worried. However, I do know a little about harvesting it. If it has slowed, it may be because you aren't pinching at the right spot. You may actually be pinching off the growing point. There are several points on one plant, which means it isn't going to kill it, but it will *slow* it. You can search youtube for a video on how to prune, bc a visual helps! Look at the stem, and notice how every node has two leaves on each side. If it were pinched at one of those points when it was younger, it would have made two new branches/stalks on each side of the main stem. Now, look at the tops, and make sure you are only cutting the stem off at a point right above these tiny little leaves, which will be the new growth of stalks. Basically, you will only be cutting off the top 4 leaves. You can also cut your leaves off the stem, as long as you are removing the older leaf, not the new growth at the junction. Hope we can both figure out what is wrong with our roots!!

Random dark spots on branches are not a concern, but a dark brown to black lesion near the soil line can be a sign of fusarium fungus. Infected plants slowly wilt to death. The Nufar variety is resistant, but it's such a hit and miss disease that I grow what I want and hope for the best.

No matter how well I keep my plants pinched, they won't last the season, especially the Genovese types. I start seeds 3 times -- April, June and July -- to always have new leaves coming. However, the small-leaved strains seem less intent on blooming, in my experience.