IMHO...
Tangibles
Of the Digiluxes mentioned... (not considering any other Leicas?)
D2:
1.) Known best for its lens (stellar). NatGeo photogs were fans of the D2.
2.) It does have an electronic rather than optical VF (which drives me mad).
3.) Watch out for failed (Sony) sensors. It is the D2's weakness.
4.) Great camera -great prices today.
D3:
1.) Lens not as good, but it does incorporate the 4/3 mount -so you have quite a lot of selection.
2.) Optical VF, but at the cost of the addition of a mirror: rather un-Leica like, but very Nikon SLRish. Bulkier.
3.) New sensor. Not familiar w/ any reports of sensor issues.
4.) A good bit more expensive.
Nikon...
D5000/5100
Great cameras right out of the box. And that is pretty much that!
Keep in mind that the AF is driven in the body on these -so watch interchangeability there!!!
As far as lenses, the 18-55 kit is remarkably good, but I would recommend picking up a fast 35 or 50 prime as well.
For the extra money, I'd recommend a 7000.
Intangibles
Yes, Leica is arguably the B&o of the camera world. I always find such striking similarities to the two. From manufacturing, sales, support, etc... Leica is certainly more of a lifestyle product rather than the "blenderesqueness" of Canikon.
There is a price to pay though. They are expensive (can be very expensive). They are often classified as quirky, slow, often buggy -but when they are on, there is nothing like them. Using them is more like enjoying a fine wine and a cigar than chugging a beer and puffing a fig. If I wish to slow down, take in the world around me, and take some memorable pictures -I grab a Leica. If I am running out the door to a sporting event, birthday party, etc... -I grab a Nikon.
There is so much more to it than just this brief discussion, but they are both fantastic brands and you would not go wrong choosing either. Just remember: they are really just a tool. How much enjoyment you perceive from using them is measured in more ways than just the picture.