If I start seeing more of this on this plant or others what should I do?

Then you'd have to ID many more symptoms to try to narrow down the cause. Assuming you have corrected for the ones you listed by eliminating over-watering and over-fertilizing and using a good draining soil-less mix then you'd be looking for signs of pests like fungus flies or aphids, looking for sins of injury to the stem or branch, good air circulation in the area (why many use a small fan), etc.

Blowing up you photo I sees signs of mold growing on the soil surface and some inverse cupping of the other leaves - both signs of soil kept overly wet. And since more seedlings are killed by over-watering/overly-wet soil than by most all other causes combined that's where I'd put my bet based on the info so far.

Dave

That plant one day later:

I did end up noticing it on two other tomato plants. I pulled those limbs off before they got to this point. I should add that it starts at the lower leaves/limbs and works its way up.

Look at the stem in this latest pic (couldn't see the stem in the others). See the brown band right at the soil line? Looks like mild case damp off. Over-watering and inadequate air circulation are the primary causes.

For future reference never leave a damaged or diseased leaf or branch on a plant. Remove it as soon as spotted. Leaving them in place like this only encourages spread of the problem whatever it may be.

Dave

http://faq.gardenweb.com/discussions/2766553/what-is-the-dreaded-damping-off-disease-how-do-i-prevent-and-or-trea

Noname, overwatering and too wet soil can be a problem, but only you can determine if that's the issue at all. You know how the soil feels, how often you've watered.

That stem has died, snip it off asap.