Without knowing where you fall as a photographer I'll just start at the beginning.
1. Get rid of the kit lens. It's usually a piece of junk. Get either a 50mm or 35mm prime lens with a wide aperture. It'll be compact, sharp, and it forces you to move around your subject and explore different angles physically, without distortion. The wide aperture (1.4 to 2.8)will also let you rack the background out of focus easier on a digital (sensors don't create that buttery softness as well as film does. Protect it with a clear or uv filter.
Nikon 50mm 1.4G
2. Fast SD cards. These will write the image to the card much faster than a generic card and keep you from potentially missing a shot because your card can't keep up.
3. A good strap. I still get annoyed at my stock strap when i have it slung across my chest for safety and can't swing it up quick enough. Try something like this BlackRapid
4. A decent bag. This depends on your own personal needs and tastes. Shoulder bags, backpacks, rolling cases. Pick something that can grow with you, with room for more lenses and accessories down the road. Just don't let it scream "Hey look at my expensive new camera! Come steal it!"
These are pretty much the must have essentials. As you explore the art of photography you'll start to encounter situations where you're going to need a specialized lens, a flash, or you might want to invest in a nice tripod.
I'm a huge fan of the cheap, fast and sharp Nikon 35mm f1.8G AF-S DX.
Nice.
To sort of add on what Joe is saying, but with a different outlook.
Lens: The kit lens of the D90 is actually solid. Meh at a variable aperture, but you get decent range with the 105mm focal length. I recommend getting a prime as well, but to save money, I recommend the lens everyone should own at one point, a 50mm 1.8. Since the D90 has a built in autofocus motor, you can save some money with lenses because you don't need AF-S
http://www.amazon.com/Nikon-50mm-Nikkor-Digital-Cameras/dp/B00005LEN4/ref=sr_1_1?ie=UTF8&s=electronics&qid=1268299980&sr=1-1
Flash: SB600 will do the trick. Get that and a pc cable to get some really interesting off camera flash shots. A fast lens will get you so far, but at a certain point, you're going to want to control your lighting.
http://www.amazon.com/Nikon-SB-600-Speedlight-Digital-Cameras/dp/B0002EMY9Y/ref=sr_1_1?ie=UTF8&s=electronics&qid=1268300757&sr=1-1
Card: I agree with Joseph. A card's speed is very important, especially when you take into account that the D90 also shoots 720p video. To be able to shoot the video as well as limiting buffer time between continuous shooting, you want a class 6 card or higher. I use 8gb C6 Transcend cards.
http://www.amazon.com/Transcend-Memory-TS8GSDHC6E-Frustration-Free-Packaging/dp/B001ECQVSS/ref=sr_1_2?ie=UTF8&s=electronics&qid=1268300161&sr=1-2
Case/Bag: Also agreeing with Joseph, bags are preference. It also depends on your uses. A couple of choices are
Thinktank(Good low profile bag so you aren't announcing what's inside)http://www.amazon.com/Think-Tank-Disguise-Functional-Saddlebag/dp/B0016L5S04/ref=sr_1_3?ie=UTF8&s=electronics&qid=1268300262&sr=1-3
Then there are messenger style camera bags like Crumpler. Then there's a wide array of bags available from lowepro. I personally use this backpack style Caselogic camera bag, as it can hold my laptop as well.
http://www.amazon.com/Caselogic-SLRC-206-Camera-15-4-Inch-Backpack/dp/B002DW99H8/ref=sr_1_3?ie=UTF8&s=electronics&qid=1268300455&sr=8-3
But if you are looking for a straight camera case. This is by far the coolest I've seen. Pricey, but awesome.
http://skytoptrading.com/
I'd also recommend a battery grip so you can have longer shoots. You can hold 2 Li-ion batteries or multiple AA's to keep your camera alive at crucial moments. Off brand does a decent job, so that'll save you money. Probably doesn't have the additional controls nikon brand ones would have, but it serves the main purpose.
http://www.amazon.com/Opteka-BP-D80-Battery-Nikon-Digital/dp/B000Q7CLUY/ref=sr_1_7?ie=UTF8&s=electronics&qid=1268300597&sr=1-7
For tripods, I'd go with either Velbon or Manfretto. You don't want to cheap out on a piece of equipment that's responsibility is to keep your 1000 dollar camera from falling 5 feet to the ground.
HUGE second for the 35mm f/1.8 lens. Super sharp wide open, and cheap to boot! Lets me take most of my indoor photos without a flash at 1/160 and ISO 2000ish, which gives completely acceptable noise. LOVE that lens. VR can never substitute for raw lens speed.
Strong second as well for the fast storage. Absolutely critical when shooting quickly, since I find I can fill the buffer quite quickly.
I found the SB-400 to be completely adequate for my needs. Simple, reasonably fast bounce-capable flash that's small, light, and cheap.
Finally, a second for the aftermarket strap, unless you like broadcasting "Steal me!" in bold yellow letters. Also a lot more comfortable. There are a ton of good ones out there.
In general: Future proof yourself. Cheap gear is rarely pleasant to use and loses 60% of its value upon purchase. High quality gear is a joy to use and will still be worth almost what you paid for it should you ever have to sell it.
You need a tripod. Tripods open up so many new photographic possibilities I'm hesitant to even call them an accessory. Tripods are one area in particular where you cannot skimp and still get a useable product.
Legs: Carbon fibre is delightfully light but pricey. If cost is a concern or you won't be hiking long distances with your tripod, consider heavier and cheaper aluminum legs. Similarly, 4-section legs sacrifice stability for decreased size and are exclusively for those who need a smaller tripod for travel reasons. Maximum extension height without considering the centre column is of great importance. You want the camera to sit very nearly at eye level at full leg extension without having to extend your centre column at all, as wobbliness increase exponentially as the centre column gets raised. Minimum height is almost as important for non-macro photographers and doubly important for macro photographers. Macro shooters tend to find themselves crawling on the ground on a regular basis - it's imperative that their tripod be able to follow.
Gitzo is the brand to buy for high quality legs. They couldn't build a useable head if given a thousand engineers and an unlimited budget, but their legs are top notch. Manfrotto makes excellent if heavy/large legs. They're starting to come out with carbon fibre legs that deal with the heaviness but still remain terribly large even when fully collapsed. Giottos, Acratech, Velbon, Slik et al do not produce consistently quality products and cannot be trusted.
Heads: Ballheads are the best all-around head for everyday use. Other heads (geared, 3-way, Wimberly) have their uses but are all highly specialized for these uses. Arca-swiss style mouting systems use a rail attached to the camera that fits into a trapezoidal space on the head. It's superior to all other mounting systems in that the use of an L-bracket on the camera allows for quick and painless switching from landscape to portrait orientation without requiring the ballhead be set at a 90° angle (and so highly destabilized).
Markin and Really Right Stuff (RRS) make the best arca-swiss compatible ballheads. Higher end Manfrotto ballheads are also quite good, but as Manfrotto insist on its inferior mounting system (RC0/2/4 etc.) you would have to replace the mounting plate on the ballhead with a 3rd party one before using it. This would add significantly to the cost of the head and make a more expensive Markins or RRS head the better choice at the pricepoint. Be sure to invest in a Kirk or RRS L-bracket for your camera.
Do not be afraid to buy tripods and heads used. Testing them prior to buying is of course required, but they're delightfully simple devices and you can test every joint and knob in a 5-minute once over. Many of the higher end brands I've suggested also carry a lifetime warranty that you can take advantage of should you manage to break anything.
1]a 70-200 vr zoom.
2]and a wide prime lens.
don't throw away the kit zoom.
they might seem expensive but they hold their value
3sdhc cards fast one's[higher the class the faster the card]
.i actually prefer lexar and kingston more value for money
4]the rest(tripods/flash etc) try not to buy them until you need them .and for a tripod i recommend one of those crappy 15$ no brand stuff.just so you can figure out what you want in a tripod
get a solid 50mm 1.4 (top of the line nikon = $500) and a 2.8 zoom lens like the 24-70 (like 1.7k) alot to pay for a lens but you will be able to keep it forever and it has a superior performance of course there you are paying for ED full frame glass but, definitely ditch the kit lens, and buy UV filters for the front they protect your expensive glass and filter some UV to make everything better, and maybe the battery grip if you don't mind getting looks from people. and always carry your lens hood.
I shoot with a D90, doing commercial and portrait work.
Lenses:
-the 35mm f/1.8 that people have been mentioning is rock solid and takes beautiful pictures, as an added bonus it weighs practically nothing and it's cheap. I'd be happy throwing that on my camera for the whole day
-A telephoto lens. You'll need it if you want to shoot sports, nature, or more professional headshots (headshot pros will use huge 300mm 2.8 lenses to get the right perspective and throw the background out of focus) I use the "Nikkor 70-300 VR"http://www.adorama.com/NK70300AFVRU.html, it's one of Nikon's best kept secrets, a really awesome lens. Or, if you're looking to save money here, the 55-200mm VR is cheaper and more portable
Tripod:
-a really good tripod is the most important thing you'll buy to get tack sharp, professional results. I'd look at Gitzo or Manfrotto legs and a Really Right Stuff or Manfrotto ballhead (ballheads are more convenient than 3-way heads) Buy the best you can afford, it's an investment and you'll use it pretty much every day you shoot
Cards:
-Get fast cards. I really like the high-end Sandisks
Flash:
I'd defer to David Hobby over at Strobist for all things off camera flash related, it's where I learned.
Other stuff:
-Any bag you like from ThinkTank
-A solid camera strap made from recycled car seatbelts from Photojojo.
All of this is a solid kit that should last a long time and be incredibly versatile. Good luck!
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Without knowing where you fall as a photographer I'll just start at the beginning.
1. Get rid of the kit lens. It's usually a piece of junk. Get either a 50mm or 35mm prime lens with a wide aperture. It'll be compact, sharp, and it forces you to move around your subject and explore different angles physically, without distortion. The wide aperture (1.4 to 2.8)will also let you rack the background out of focus easier on a digital (sensors don't create that buttery softness as well as film does. Protect it with a clear or uv filter.
Nikon 50mm 1.4G
2. Fast SD cards. These will write the image to the card much faster than a generic card and keep you from potentially missing a shot because your card can't keep up.
3. A good strap. I still get annoyed at my stock strap when i have it slung across my chest for safety and can't swing it up quick enough. Try something like this BlackRapid
4. A decent bag. This depends on your own personal needs and tastes. Shoulder bags, backpacks, rolling cases. Pick something that can grow with you, with room for more lenses and accessories down the road. Just don't let it scream "Hey look at my expensive new camera! Come steal it!"
These are pretty much the must have essentials. As you explore the art of photography you'll start to encounter situations where you're going to need a specialized lens, a flash, or you might want to invest in a nice tripod.