Also another one of these is in a tomato grow bag, also with a bottom-self-watering system.

I've been finding that ever since the 6-inch pot phase, on to today, the older/lower leaves of the plants turn yellow and brown and develop some spots. I've looked at pictures of blights and septoria and I can't say with any certainty that my plants match the pictures. I could also just be over-watering and should perhaps let the soil dry out a bit between waterings? I don't water from the top, only fill the reservoir and let the wicking happen on its own.

The tops of the plants all look green and lush.

I've gone ahead and trimmed off the ugly looking bits, but I've not tried much to remedy the issue. I haven't used any fungicide yet.

I have a second grow box with a newer set of the same variety (seeds planted March 25). These seem to be doing okay, but I'm seeing hints of the yellowing on the first real leaves while the second set of leaves look good.

I'm in the SF Bay Area, so the air is moist and the temperature is generally between 50-70 degrees. The plants get about 8 hours of direct sun a day.

gallery: http://imgur.com/a/HKDgI

Second, yellowing of leaves alone - any leaves - is not a fungus infection indicator and I don't see any signs of anything else fungus-wise in the photo.

But it is a very good indicator of over-watering and insufficient nutrient problems.

Container plants require regular feedings - weekly - and organic fertilizers, unless they are liquids suspended in water, don't work in containers since there is no active soil food web there to convert them to a form useable by the plants.

Trying to grow in containers using only organics requires a very different approach than organic gardening in the ground.

Your plants need less water and more nutrients.

Dave

Looks like overwatering and underfertilizing to me.

The yellowing alone isn't concerning me so much as the spotting (perhaps I should've posted one of the other pictures)

The plants will probably outgrow the growbox, but this just my first attempt to see if I can even keep something alive. (also the growbox instructions said to plant 2-3 tomatoes... but perhaps it was intended for a smaller variety)

Here's a picture of one of the younger plants still in the 6-inch pot.

But it is the over-all health of the plant that should be the focus so that it can resist disease and pest problems. And with your plants the severe yellowing should be the primary concern as it indicates a more serious problem than the spots I see in your photos.

While it is possible that some of the spots in your photos could be signs of Early Blight it is not possible to say for sure from any of the photos. Removing the affected foliage and spraying them with a fungicide sure wouldn't hurt them, but it is the nutrient ad water issues that really need to be addressed.

They are growing in a somewhat stressed situation already from the over-crowding and the appearance of the soil condition in your pics so providing them with sufficient nutrients in a form the can use will go a long way to improving their situation.

When one is new to growing tomatoes and a problem develops the inclination is always to jump to the conclusion that it is a disease. But 8 out of 10 times the problem is actually related to the growing conditions rather than any disease issue. When the growing conditions are less than ideal to begin with then those odds go up even more.

Hope this helps.

Dave