Go for either a D7000 or a D300s. The D7000 has 39 AF points, and the D300s has 51. If it is resolution that you are looking to one-up, then the D300s or D90 would not quite "up the ante" enough (at least for me, if I plan to put a significant investment into an upgrade, I would go for the gold). Currently, the D7000 has the highest resolution sensor in Nikon's APS-C lineup (16.2 MP).
If money is the issue, the D90 is certainly a step up from the D3000. The body os slightly larger, there is an LCD display on the top, behind the shutter button, allowing you to check and/or change the settings without using valuable battery power with the large 3" LCD on the rear.
This is coming from the perspective of a D7000 owner. I have had it for several months now, and I can tell you that it exceeds my expectations. If money is not an issue, than consider te D7000, or if resolution is not a top priority, go for the more durable D300s. It has a higher frame rate than the D7000 (7 vs 6 fps).
Worst advice ever and cost is a factor if you read the OPs post. He has a lightly used d3000 and you are recommending bodies that are double or more the cost. Although since this thread was made the d5100 came out. But for the price I would maybe go for the d90 still to have the in body af motor.