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I really like my D90 and the 70-300VR. I wish I had the 16-85...that's a perfect kit for general photography. Add a 50 or 85 f/1.8 and you're done!
The D90 is old so its image processor isn't as advanced as the latest cameras. Still, it can do a nice job. By far and away the best thing you can do for your color is to learn how to set a custom white balance, and Nikon makes it very easy. First, get yourself a good quality WB reference such as the Digital Gray Card by Robin Myers Imaging. It's 15 dollars US, and he mails anywhere. Second, learn the process of setting WB...
1. set the WB to "Pre" and release the WB button.
2. press and hold the WB button for 2 secs, until "Pre" starts flashing.
3. frame the WB card, angled to catch the light and filling the viewfinder, and press the shutter.
That's it...you're ready to shoot with your custom WB. The WB card slips into your back pocket and you're ready to go. It's so easy that I do it every time I step into new light.
After WB, the next thing I would explore are the base Picture controls. You should experiment a little by taking several images of the same scene with different Picture Controls. Here's a tip...you can change the picture control quickly by pressing the info button twice. That gives you access to the Quick Settings menu that's at the bottom of your regular LCD status screen. One of the choices is Picture Control. Press the info button twice, then use the left-right controls to select an option to edit. Then press OK to actually edit the option. The camera will remember your last choice, so if you're playing with picture controls then you can just press info-info-ok and you're in the PC menu.
The one thing people complain about with D90 JPEGs is that they are a touch soft. I've looked into this and I feel that Nikon set the sharpness settings so that you don't get any halos. Halos are bright thin lines surrounding contrasting detail. The lines aren't in the original scene...they're a result of the sharpening process. You can always edit the picture control and increase the sharpness one or two clicks and see if you like the results. The Landscape PC already has sharpness increased, so when experimenting with PCs just keep that in mind.
The D90 has just under 2/3rd stop headroom. That means that when the "Highlights" function of image review starts to show you clipped highlights (blinkies) due to overexposure, the actual RAW data is likely just fine. You can spot meter a bright white object, like copy paper, set your Exposure Compensation to +2.3, and get a nice bright white without clipping. If you were shooting RAW you could go to +2.7...this is one of the reasons why people shoot in RAW.