If you're looking to go high-end amateur, or low-end professional, I'd have a look at the Nikon D100, and the Fuji S1 Pro and S2 Pro.
The S1 Pro you can pick up used these days for around $750 or a little more, the D100 for a tad over a grand, and the S2 Pro is also around about a grand or so, maybe a little more.
You might also want to consider the D70, and while these are not out yet, when they hit the market (in just a couple of weeks from what I've heard), they'll have a street price of around $1,000 brand new with full warranty. However, there's also a whole new range of lenses & flashes out for them that are slightly more expensive than those already out for existing Nikon-based SLR cameras. Also, if you decide to get more serious in the future, the D70 doesn't have the expandability of something like the D100, where you can buy a vertical grip & battery pack. The S2 Pro has a built-in vertical grip, and I think the S1 Pro does too.
Of course, you'd still have to invest in some lenses (but you can get a nice pair of AF Nikons for as low as $200 new for both of them - the 28-80mm f/3.3-5.6 AF-G, and the 70-300mm f/4-5.6 AF-G). All three of those cameras, as far as I'm aware, have a built-in flash. I know the D100 does, I'm 99% sure the S2 Pro does, and I THINK the S1 Pro does too. But I would still invest in a separate dedicated flash. You can pick up an SB-50DX for around $100-150 bucks used.
I'd pick up some UV filters just to keep your lenses protected if not for optical improvement. It's much cheaper to replace a $10 filter, if it gets scratched, than it is to replace a $150 or more lens.
Then, just get a good solid tripod and you're good to go! Also, if you're thinking about buying online, if nothing else, the tripod is the one thing I would actually want to go down to the store and play with. Even with different tripods that are the same make & model, there are variances, and a cheap low-end tripod (like the freebies they give away with $300 camcorders) are no good for serious photography. A light breeze makes them judder, losing much sharpness on those shots where you need to keep the shutter open more than about 1/60th of a second.
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Axe
The Reptile Rooms