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I own a D3100 and love it... I only wish I would have got the D7000 because it has an internal AF motor for a larger range of primes. However besides the internal motor absence the D3100 does everything the D90 does.

A D7000 would not disappoint in my opinion.
Quality is ambiguous, but here are some facts: 14 vs. 16 megapixels, 11 point vs 39 point AF (this is important), Twin card slots and a higher ISO range. And no dumb-it-down "Guide" feature.

I would recommend trying them out at a store to get a feel for the size, ergonomics, and button layout. I was deciding between the d5100 and d7000 because of the shared sensor and cost. After handling a d5100, I did not like the layout at all- in particular, the ISO adjustment is buried in a menu somewhere, although there is a programmable button on the left side of the body that can be used as the ISO adjust.

For a professional photographer, there are a few more factors to consider when making the switch to digital:

Do you already have a vast library of lenses? Are they compatible (mount, AF motor, etc.)?

Ergonomics- which body feels the most intuitive, or which one would you want to learn?

Crop factor/sensor size- consumer-level DSLRs use an APS-C sized sensor (Nikon calls it DX) which results in a cropped image compared to a 35mm frame (Nikon calls it FX). The Wikipedia entry on crop factor (en.wikipedia.org­/wiki­/Crop­_factor) does a good job explaining this, in particular the effect on the field of view on lenses. It's just something to be aware of, especially if you're used to how a particular lens should behave for a particular shot.

These are just the tip of the iceberg, but are the most important things I can think of as a non-photographer.

If your wife is used to taking pictures on a professional film SLR then the controls of the D3100 will probably be a pain to her since a lot of the things you would want to control are hidden in the menus instead of changed with buttons and dials. I would get at least the D90, though if you can justify the extra cost the D7000 is a pretty nice upgrade to the D90

I'm interested in your choice. I would have recommended the D7000 which I own. I've had the D5000 which is similar to the D3100. Without the motor on camera it limits the lenses you can use with autofocus.

The D7000 feels more pro then most prosumer camera's I've had or held. Nikon did some good things with this camera. It leaves me wanting in a few areas such as video. I'd love to have a 60fps HD mode but we do not have it. Maybe that will come someday in the form of a firmware upgrade.

I have to echo what "2manywires" said. The D3100 is a very good entry level camera but the internal motor and the extended ISO range make the D7000 a much more versatile camera. If you already own an AF lens or plan to buy and AF lens, it's a no-brainer. The D7000's internal motor is surprisingly (to me) powerful and precise. I've also been surprised at what I can do with the D7000's extended ISO range. I hate the way flash pictures look, I would much rather use natural light and the D7000 greatly expands the range of pictures you can take without a flash.

I have a D7000 and about 3 or 4 film cameras, one of then a Nikon SLR. I have some lensesthat I delibarate purchased in order to use them in both cameras.
For a professional film potographer I think that the main diferences shifting to digital is the serious big diferences in how the light is percieved by the medium (film vs sensor in digital) and your wife will spend a lot, A LOT, of time trying to find out how to make the digital one to show results similar to the film one, and to be even more fatidical, there is a world of diference between every brand of film, so the fine tuning that your wife will eventually find will be only valid for the brand of film that she uses most of time. This is not an easy task.
When you shoot film, you set your ISO for a whole roll, and how colors are percieved depends on the brand of the film. In digital you can manipulate these two as aparameters, for ISO you can even set "auto ISO" (but your wife will probable think that "auto ISO" is the devil itself) and in the D7000 you can get ridiculous high ISO and still have decent results (I hink that a pro film photog will even miss the grain, but the truth is that digital noise is a pain and is not even close to the beautiful grain noise from high iso film). The other parameter is the white balance that can be something new for film photographers (this can also be percieved as the devil wife) sadly this control is a new necesity.
The main diferences between an entry level and a pro camera (being pro-suber or "advanced amateur" cameras right in the middle) are durability and manual fisical controls (instead of controls buried in some dark and infinite menus), nice cameras like the D700 even have user banks to groupo settings that are one of the features praised by pro people.
Now, talking obout the D3100 and the D7000, for your wikfe the answer is a no brainer, D7000 all the way.