Hi, Else. Welcome to GW. Great photos, and I love the pencil pointers.

First the obligatory I-am-not-an-expert disclaimer.

What you call 'withered spots' look to me like they might be sun-scald.

Do you water from the bottom or the top? If you water from the top and drops of water get on the leaves while they are in direct sun, the water acts like a lens and burns the leaf. [The same can happen outdoors after watering or rain.] That's only one reason why watering from the bottom is preferred.

So if water drops might have been responsible, I wouldn't be concerned about the withered spots unless they become larger or you have new ones.

Did you make drainage holes in the white cups before you potted up? I notice the other (non-withered) spots are only on the tomatoes in the white cups, and the white cups don't seem to have the aluminum foil 'saucers' the red pots have. [I pot up into 16 oz. plastic cups, and snip 3 narrow bits out of the bottom edges with kitchen scissors: it's one of those tedious jobs you can do while watching TV or talking on the phone; at first it seems to take forever, then suddenly you're done and you kind of miss it. There's probably a better way, but they do drain well.]

agree with mto, looks like sunburn and or windburn

I too think you may have some sunscald, and possibly overwatering, soil looks dark. Plants that look wilting and listless are often getting too much water, try letting them dry out some. Tiny black flies, (Gnats) are pretty common around wet potting soil. Unless you get a lot more, you can ignore them. For the most part, your plants dont look too bad to me. I also love the pencil. =)

Wow, you started seed on the 8th and they're that big? I started mine the 12th and just potted up from the plug flats since they've got their first true leaves and were getting leggy with no grow lights in my bay window. About 3" tall but didn't seem to get any more leaves, just roots. I potted them down to 1" or even on some down to the cotyledons, hope they start growing again.

I put the grow lights on last night (only a few hours) and today started them at 6am, will run til 10pm.

Other than the sunscald spots and overwatering, they look pretty good. What's your secret?

Hey we started ours on the same day :) Here's a photo of my tomatoes. It's nice to see your grape tomatoes also have a much different leaf. I was wondering about mine.

I wanted to say that if you're using the Miracle Grow Starter Mix in those cups that mix doesn't have enough nutrients in it once plants have their first leaves. I used that mix to start my seeds, then transplanted them into Miracle Grow Potting Soil (not the organic kind, and not the kind with moisture retention). Maybe over watering + lack of nutrients is your problem? Good luck with your seedlings.

Miracle grow seedling mix is too water retentive for transplants. Even worse when you reuse it. They need a much better draining mix. Aside from spots, they look like the roots are starving for air.

Thank you so much for such great responses!

Wow, yeah, you're probably right; they may be over watered. There are no drain holes in the white cups, will try to see if I can get that fixed. Maybe by tapping in a nail here and there? The red ones are great; old ones that held veggie plants from the store, and they have drain holes.
The reason I used potting mix, is that i read that this is was preferred over real soil. They must have meant for the initial planting of the seeds.

How do I fertilize? I do have some Miracle Grow powder fertilizer (mix w/ water) for tomatoes; 18-18-21. Should I just use that? How often and for what duration of time? I know that if you overdo fertilizer, you'll end up with tons of growth and poor fruiting.

It is possible that some leaves may have gotten wet, I can't remember. I'll be more watchful to keep that from happening. Most of the new growth looks very good, though some limp leaves that seem a bit better today, and some leaf curling on a few leaves. No aphids, like I said.

Wow, I am so excited now; I thought maybe these plants were toast! I had been so excited about these plants, because I spent a lot of time selecting the seed varieties I ended up with, and trying heirloom for the first time. I also was planning on sharing my "leftover" plants (won't need all of them) w/ friends / family, but I cant's bring myself to give away diseased plants. Maybe these aren't diseased after all.

If you think my plants are doing well, I don't know whether I did anything special. I seeded two seeds in each egg carton pocket, then snipped off the weaker plants (skinnier stems) after they were about an inch or so tall. I did put plastic foil w/ holes over the egg cartons and tooth picks for support to keep the plastic a little higher. Used this the first week or two after seeding, for warmth, until the plants started hitting the top of the plastic. Removed the plastic at that point. Watered w/ spray bottle to avoid disturbing the tiny seedlings, but graduated to a squirt drinking water bottle later. They were in a window on the north side in the beginning, while the plastic was on, but then moved them to a sunny window on south side. I kept turning the trays when they leaned toward the sun to keep them growing straight. I don't own any lamps, just using natural light.

I'm curious, Else, to get an update on how your tomatoes & basil are growing. Anything interesting to report?

Agree with Capo - MG starting mix is too water retentive - hence the black flies. The mix is heavy and is not letting your plants' roots breathe.

Look into Al's 5:1:1 mix. I have had the best results of my long growing career with his lighter mix. (Basically it's 5 parts aged pine bark mulch, 1 part sphagnum peat moss and 1 part perlite. Depending on the plant, I will exchange compost for the peat.)