use aperture up to 8/11, anything above that will not yield good results due to diffraction. and it's simple: the lower the focal length and the higher the aperture the more depth of field you have. at 18mm you'll get a very deep DOF even at 5.6.

If you mean by colouring certain parts of the image and leaving the rest b&w then no, easier to do it post anyway.

Set you camera AF system to spot metering, then use your dial to point on the subject you want in focus. Ensure you depth of field is sufficient for your needs, i.e F2.8 of larger.

All Nikon lenses are compatable as they all usethe F mount, only the newer AF-s lenses will autofocus though.

http://support.nikonusa.com/app/answers/detail/a_id/17162/session/L2F2LzEvdGltZS8xMzE5NzkyMTk3L3NpZC9Ud2lpTEdIaw%3D%3D

SB 16 is just the flash body designation, there are two couplers AS8 and AS9, AS9 is for hotshoe mounts and the SB16 with that coupler is designated as a SB16B, this will work with a D3000. The AS8 coupler is for older F3 mounts. So it depends on which coupler you have.

There are loads of fish eyes available, the 10.5mm being one of them.

Is this with all lenses or just the lens that comes with the camera? If it is the lens you have with the camera you might have set it to manual. Look at the swich on the side of the lens which says 'M/A' or 'M' if it is switched to 'M' then have set the camera to manual focus. Another reason it could be is that the camera has no internal focus motor and you have an older lens which doesn't have a motor, like the 50mm 1.8D then the lens won't be able to autofocus.

The D5000 has been replaced by the D5100 which is much better. As for accessories for the camera, it depends what kind of thing you want to do with it. It takes an SD card, I would suggest buying a class 10 card which will allow you to record HD video. You can buy lots of lenses for the camera, though it doesn't have an internal focus meter, so you will only be able to focus the lens manually. These are generally older lenses, there are lists about as to what lenses work on the camera. You can buy a flash, which is good for certain things and a tripod. though these 2 things are not essential.

A lot is down the kind of money you want to spend. I suppose the traditional focal length for portrait lenses is around 70mm to 135mm. Though you can use a 50mm (all this is 35mm without x1.5 crop). So For a 50mm 1.8G or 1.4G (75mm crop) should work as a nice portrait lens. Unfortunately the Nikkor 85mm 1.8D (127.5mm crop) won't autofocus, when used on the D5000 (though it is a wonderful lens, when fixed to a DX camera). As for zoom lenses the 24-70mm 2.8mm is great (36mm-105mm crop).

Yes and it took me about a minute to find it, when I typed firmware update Nikon D5000. I believe it is firmware update 1.002 but will let you find it.

what kind of photography you are doing ?

No, it does not have an external microphone input.