Man, I've been exposed to so many little fictional deities over the years that I'm not sure I'm not forgetting my favorite. However, if I had to take a few stabs in the dark:
Flute/Aphrael from David Edding's Elenium [http://en.wikipedia.org/wiki/The_Elenium#The_Diamond_Throne] series. A wry-natured (as Eddings characters tend to be) little deity but rather intimate/caring in that she tends to prefer to be reborn amongst her mortal followers so she can keep a better eye on them.
Haruhi Suzumiya - Actually, it's debatable whether she's really a deity or not (only 1 of 4 of her fellow club members seem to think so) but she's certainly an interesting concept.