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Whenever I view my 12MP photos on my computer at 100% zoom (they're roughly 4200x2400), there always seems to be a lot of grain and noise to the image quality. What, specifically, causes this and what can be done to fix it?
Equipment:
I'd prefer not to use any software like Photoshop to remove it (because it's more of a workaround than an actual fix, and Photoshop isn't really in my workflow).
What you are seeing is an image noise -- random fluctuations that affect sensor pixels and cause them to measure value a bit above or bit below light that actually comes to the sensor.
The main factor that increases noise is how much is the signal from sensor aplified. There are two things that influence this:
Size of sensor pixel: if you have 12 megapixels on 24×16 mm APS-C sensor, each photosite is smaller that it would be on say 2 megapixel APS-C sensor. Therefore is catches less light and needs more amplification. Similarly, 12 Mpix D90 sensor has significantly larger photosites than 12 Mpix compact camera sensor, and thus has less noise. This is one reason people buy DSLRs instead of compact cameras.
ISO setting on camera. Basically, ISO says how sensitive you want the sensor be, so higher ISO means more amplification. You'll find that lower ISO settings produce less noise in images, and on D90 noise probably won't be noticable at ISO 200 or so.
Obviously, avoiding noise has it's drawbacks, because larger-sensor camera are bigger and more expensive, and using lower ISO might means either opening up aperture and losing depth of field -- provided that you have fast enough lens (fast lenses can also be expensive). The other option is longer exposure time that means risk of blur from camera shake or moving subjects.
Sometimes, as rfcusa notes, in 12 Mpix images certain amount of noise only matters when you're examining it in 100% magnification on a computer. Unless you intend to produce huge prints, these viewing conditions happen very rarely.
Most DSLRs are somewhat grainy at 100% digital zoom.
I use the same body and lens and the best thing you can do is set your ISO low (I keep mine around 200) to prevent noise. The D90 is also acceptable in noise up to 1600.
If you are having to digitally zoom on your computer to get the right composition you probably need a different lens. Maybe you should invest in a good telephoto lens like the a 70-200 2.8 or a teleconverter.
If you're shooting indoors, and not using flash, the kit lens is typically much to slow for many, many shots. Your camera (or yourself) is probably raising the ISO and this is noise due to the increased ISO. Either get flash, a faster lens, or shoot somewhere with more light.
A certain amount of this noise is present in many normal, high quality shots when viewed at 100% - depends strongly on sensor, light, and ISO. Unless you're printing at 100%, don't fall into the pixel peeping trap.
The D90 (and other cameras as well) has a feature that will automatically boost the ISO in order to get the correct exposure. If you turn this off, then you can set the ISO manually and thus cap the noise levels.
Of course, if you do this, you run the risk of not getting the correct exposure. But this is where a faster lens (as @rfusca mentions) helps.
One thing that hasn't been mentioned so far is the effect of the software you use to import images. If you're shooting RAW, your RAW processor may be applying some sharpening to your images by default, which adds noise.
I know for a fact that Adobe Lightroom does this, very annoying when a super-sharp image suddenly looks noisy for no apparent reason. For Lightroom, this can be fixed by creating appropriate import presets, and I would imagine that most other RAW converters also have a facility to modify the default sharpening.
EDIT: As Francesco says below, if you're shooting JPEGs, you might get better results by reducing the amount of sharpening applied in-camera. I have no idea if this is possible specifically with a D90 though.
The reason for visible noise is not enough light.
The description below is an inaccuratee simplification but it helps to undertake the issue.
There's always some level of noise, when you're photographing something nice and bright there's a lot of real data to overpower the noise.
When you photograph darker scenes the power of the real image is closer to the power of the noise and so the noise become visible
To see the effect just take a photo in direct sunlight and see there isn't much noise.
To reduce noise you should try to get more light into the camera - you can use a wider aperture (lower f number), longer exposure or add light (for example with a flash)
When the camera does not have sufficient light, it will usually compensate by increasing ISO (from a baseline of 100).
You can fix this by making sure your scene is well lit.
Your lens is faster when zoomed out, so zooming out and "zooming with your feet" will allow the camera to reduce ISO.
You could choose to underexpose to reduce ISO.
Consider setting "High ISO NR" to "High" in your camera settings.
Consider reducing the dimensions of the images your camera creates.
