They look healthy, but I'd pinch the long ones and bring the light down to no more than a couple inches above the plants.

Zone 6 can still have a lot of freezing cold weather left. While more mature thyme plants can take our winters, these little seedlings can't take those conditions. You will have to wait until spring to harden off the plants outdoors. Do what you can for them indoors until then.

FataMorgana

Thanks for your responses - I'm going to look into pinching and will adjust the height of the lamp, it's actually been more than a couple of inches away from the tops of the plants. I'll definitely get them outdoors once it's warmer and the're bigger. I'm sure I'll have many more questions then.

If you cut the long branches back you should stick them back in the container as cuttings. They'll probably take if you mist them occasionally.

I agree with the pinching, but only to the degree that you could remove only the growing tip of the stem. Your plant is struggling to build a root system now, and needs all the photosynthesizing machinery it has, because that is where the plant's real food, sugar, is made. The plant then uses the sugar (photosynthate) to grow more leaves and roots.

The purple underleaf surfaces may or may not be typical of the species. What are you using for soil? If you're using coir or there is a significant amount of coir in the soil, it's probably being caused by what is referred to as an antagonistic deficiency (of phosphorous) because of the high K content of the coir. Anything (cultural conditions) that slows growth without reducing the plants ability to carry on photosynthesis can also cause a build-up of a purple pigment (anthocyanin) in the foliage.

Have you fertilized? With what and what strength?

Al