Dust on the sensor. Unlike film, it stays in the same place until you remove it.
I know lots of people swear by the brushes that are out there, but if I simply blow off my sensor with a bulb daily (it takes approx 15 secs), I almost never see dust spots. If I blow it off (pun intended?) for a week, then the dust spots are everywhere.
Photoshop CS2 healing brush is also a great antidote for dustspots.
Just clean the sensor routinely. Anyhow, I seem to recall dust on my film negatives, too...