I have both the D7000 and the D7100, and while there are definitely features I like better on the D7100, there is really not a tremendous difference between the two cameras when it comes to the end product.
24 -vs- 16 MP. ok fine, if you are convinced that more is always better, then sure. but, how much cropping are you going to do that you will really notice a difference?
if you do a LOT of heavy cropping, you might actually need the extra MP's, otherwise, I think you will find the IQ of both camera pretty similar.
the lack of the AA filter on the D7100 was big news, but I do not personally think it is such a huge game changer that the D7100 becomes a "must have" over the D7000.
51 -vs 39 AF points. same principle as the MP really. is 51 points technically better? yea. are you going to suddenly get shots you were never able to get before? probably not. I mostly shoot single point focus so the differences were negligible. you do get more points to choose from, and a better area AF spread. the D7100 AF system IS an improvement over the D7000, but again, I don't consider it to be some monumental super upgrade.
Misc. button placements. eh, its pretty much the same deal anytime you get a new body. there always seems to be SOMETHING that gets moved around. easy enough to adjust to with a little practice.
the D7100 is built a little better, it feels a little heftier, and does have some decent upgrades from the D7000. I would certainly never put anyone off of buying one, I love mine. that being said, I don't really think there is a HUGE difference between the two cameras. neither does a few review sites.
Snapsort
DxOMark
both of those review sites placed the D7000 and D7100 pretty close, and while the D7100 rated slightly higher on both places, the D7000 was not very far behind.
this only matters of course, if you care about what review and comparison sites have to say. I like to use them just for comparing specs and features.
Both cameras are a pretty good upgrade to your D3100, and the built in focus motor in either camera will open up a lot of older AF and AF-D pro glass at very affordable prices. To ME, the built in focus motor is the most significant upgrade, and the one that will yield you the biggest gains. the D7000 is selling at some record lows right now with the D7100 and D600 being recently released, so there are some amazing deals to be had on it.
like wise for the D7100, with a lot of people rushing to go FF with the D600 and D610. It will mostly come down to your budget. If you can find a D7100 for only a little more than you can get a D7000 for, i would say go for it. If you find an amazing deal on a D7000 with low clicks somewhere, i dont think you would be wrong for grabbing it.