What kind of light are your
seedlings getting? It sounds like the light is insufficient, so they are stretching for the light. If you don't have direct sunlight, you need to keep them less than 2 inches from a florescence light.
Once you have the correct lighting, you can strengthen the stems by gently stroking the
plants 10-15 times, 2-3 times a day. I just turn an oscillating fan on my
seedlings.
Another question is what kind of medium did you use to start your
seeds? If you used a soiless
seed starting mix (recommended), then you'll want to feed your
seedlings a very dilute fertilizer or compost tea to help them grow stronger.