I'm sure almost everyone has heard to store tomatoes stem side down. This is a short article from Cooks Illustrated about why this is better. I thought it was interesting that they did a test with the stem taped up; then it didn't make any difference which way the tomatoes were stored.
http://www.cooksillustrated.com/howto/detail.asp?docid=1173&Extcode=N1HSPFA00
http://www.cooksillustrated.com/howto/detail.asp?docid=1173&Extcode=N1HSPFA00