I planted 180 Seeds at a south facing window, in 0,2 liter plastic cups, with slits for drainage cut into the bottoms, one seed a cup. I made the common mistake to a) over water and b) to top water the planters.
As a consequence I had problems with fungus gnats multiplying in the moist soil, and a fungus disease called damping off. Fungus gnats are tiny, dark flies that hover around the plants at soil level. The flies themselves are completely harmless, but their larvae feast on the plant's roots, cutting of their life supply systems.
Damping off is caused by a fungus that grows on top of moist soil and eats away the seedlings stems at soil level, causing the plants to tip over. I was able to contain the damage by using organic pest controls:
I ordered Steinernema Feltiae Nematodes from Katz Biotech AG. These are tiny wormish parasites that introduce a bacteria into the fungus gnats' larvae, which eats them up form the inside out, breaking their propagation cycle.
Cinnamon sprinkled on top of the soil and chamomile tea for watering took care of the damping off fungi. Cinnamon and chamomile are powerful natural fungicides, plus they smell great.
Things I will change the next time starting seedlings: The plastic cups I used did the job, but where not perfect: they had too little drainage and airflow, were too small for growing plants to the size of strong transplants and they were opaque, so I didn't know what was happening in the soil. Next time I will try transparent 0,5 liter cups with plenty of holes about 3 cm from the bottom for aeration and drainage. The bottom 3 cm act as a reservoir to store water which will be wicked up through capillary action. When I see the soil drying out I can quickly dunk these planters in water, filling up the reservoirs to keep the wicking action going. Because the cups are transparent I can visually control soil moisture and root growth. This is a huge benefit, especially when you are starting seeds for the first time.
I'm melting the aeration / drainage holes into the cups with a hot soldering iron. The fumes are rather unpleasant so definitely do this outdoors.