It depends on what you need. The D90 has features like Active D-lighting (I think the D60 has this, though) and absurdly-good high ISO performance which can greatly improve image quality in certain situations. Being a second-generation Nikon, it is better than either of the other two but, of course, more expensive.
Personally, I think the video capture and live view features are gimmicks. I wouldn't take them into consideration when buying a camera.
Major flaw with the D90: you can't connect it to your computer as a USB MSC where your computer simply recognizes it as a hard drive. Currently, the yuck PTP protocol is the only option. Hopefully, Nikon will fix outright bad defect with a firmware update. I wouldn't touch it with a ten-foot pole until they do.