There is no single best product and you can burn your way through $3500 fairly easily. It will not be enough to buy a D3, and neither the D3 nor the D300 are available before November (and they'll be tough to find after November too, especially the D3). It will not be enough to buy professional grade lenses.
For a novice user, $3500
is a lot of money to invest in equipment. I'd be inclined to spend less until you have enough experience to know what you need without asking questions like this in BMW forums.
I'm a Nikon shooter, so I'll limit my recommendation to what I know. The prices I am citing are from
B&H Photo. I'm risk averse when spending thousands of dollars, and buying from a solid retailer buys peace of mind.
I could burn through $2500 buying a D200 body ($1500), 18-70 AF-S DX mid-range zoom ($350), 70-300 AF-S VR tele zoom ($485), and an SB-600 flash ($185). That leaves $1000 for compact flash memory cards (the faster the better), a bag, a tripod and ballhead (and maybe arca plates and clamps), photo editing software (I use Lightroom and Photoshop CS3), filters, and other little gadgets. A D80 would save you a fair bit of money over the D200 at $875 for that body.
Before you spend any money, read any informational articles you can find and study product reviews. Reading a book like
John Shaw's Nature Photography Field Guide would be a wise move.
Some web resources:
http://www.dpreview.com
http://www.imaging-resource.com/
http://www.naturfotograf.com/index2.html
http://www.bythom.com
http://www.fredmiranda.com/reviews/
http://www.the-digital-picture.com/Reviews/