Of course you know that the major differences are the 6MP vs 8MP resolution, Sony's four-color sensor, and the fact that the D100 uses interchangeable lenses.
The Sony also has Sony's Nightshot technology, which is way cool, and fairly different ergonomics.
From what I've read about the 828's predecessor (Mike Johnston over at The Luminous Landscape
has a lot to say about it) I think the question of whether I wanted an 828 or a D100 would be a toughie. Since I don't have any Nikon glass or flash equipment, I think that if you appeared before me this instant with both cameras and said, "Choose!" I'd probably go with the 828, simply because I don't have the cash for glass right now.
I used a D100 last week and liked it a lot, but the images I got out of it really didn't seem any better than the images I've seen out of my BIL's 828, and I'm a better photographer than he is. So for your first digicam, especially if you're not going to have a lot of money to spend on glass, I'd say the 828 would be a solid choice. I'd sure like one.