This takes care of it every time...
I always leave room in the pot when starting seedlings, for when the seedlings start to stretch. Usually, once they reach the top of the pot, I'll bury the stem, to just below the cotelydons. (the first set of leaves you see) Carefully pack the new soil around the stem, but don't be too aggressive. Leaving room in the pot for watering is pretty much a good idea, too. :thumbsup:

Can also transplant if no room in your pots to do this. Just don't break anything when doing so. :jointsmile:

Beyond that, keep an oscillating fan on 'em. A little breeze strengthens the stems.

Before and after shots: