I have a Nikon d90 and have often found that the camera reaches focus faster, with less re-adjusting and missing the focus, when I have a speedlight (the Nikon sb-600 in my case) attached.
Why is this the case? I don't know enough about autofocusing systems inside the camera but I recognise that a red light is emitted from the speedlight while focusing and that this is likely involved.
The phase detect autofocus on your D90 works by measuring the displacement between two 1-dimensional images formed on the autofocus sensor. By detecting features in these image strips and measuring their offset, the distance to the subject can be estimated. In low light it is difficult to for the camera to identify features and make a measurement as the image strips will be very dim.
Most modern speedlights (such as your sb-600) have an "auto assist lamp", which is usually implemented as a red LED matrix that projects a grid pattern over your subject. The projected grid lines are easy for the AF system to pick up and measure displacement as you get a sharp peak on your image strip where a grid line crosses.
To augment Matt Grum's answer, one of the reasons the emitted light is red is that it is typically the least sensitive band of colour in our vision. This is often used in lights and software interfaces used in astronomy, so as to not cause glare in the darkness. When you're shining a dim red light at someone, it won't have the "blinding" effect that a strobing AF flash will (such as the small Canon 270EX which uses a series of normal flash strobes to auto-focus) or a torch, for that matter.
My D90 has a focus assist light built in. You turn it on or off in the menu. Try using it without the speedlight and see if it improves your focusing. I discovered it by accident when I was doing some stop motion photography and stepped away from the camera. You don't notice it as much through the viewfinder.
The speedlight or in-camera focus assist can't work outside of the range of the lamp, which is I believe around 13 - 18 feet, depending on aperture. Check the manual.
As Matt points out, auto focus systems require enough contrast in order to detect the image of desired focus. Two limitations do exist, however. One is the distance of effectiveness, as Jeff points out. The other is that with projected grid lines, what you really want in focus may not be in the same focal range as items in the grid that your auto focus picks up on.
There are now accessories you can buy to assist with focus that provide a single point of light (rather than a grid) and have an effective range of over 100 feet. With those you can get the fast focus you want, on exactly the subject you want, and do so throughout the effective focal range of your lens. They use the same principle as your speedlight - providing that point of contrast for the auto focus to pick up on.
