I would suggest that you hold off on most of your purchases until you get a better feel for what kind of photography you like doing. The only thing I would suggest from the start is to try to get a body only D90 and getting an 18-200mm lens. I own both the kit 18-105 and the Sigma 18-200VR and I haven't seen any noticeable difference in quality between the two, while the 105-200mm range comes in handy a LOT for me (I do travel photography mainly). Keep in mind that the Sigma lens tends to 'slide' out if you hold the camera towards the ground, which is a bit annoying, but it is quite a bit cheaper than the Nikkors.
Also, make sure you put UV filters on all your lens to protect them.
The other things, as mentioned above (but with a few caveats):
1) Spare battery - I've never personally seen a need for a battery kit, but a spare battery fully charged has saved me on a number of occasions.
2) Prime lens - A F1.8 prime is definitely very useful, and can be bought quite cheap. The 'nifty fifty' 50mm F1.8 from Nikon is great, but keep in mind that it's actually more like 80mm on your cropped sensor, which is better for portraiture. For day-to-day use, I prefer the Nikon 35mm F1.8, which approximates a full frame 50mm. Most of my favorite photos are shot with one of these two primes.
3) Flash - the built in flash on the D90 is a bit crap. Even if you're not interested in off-camera flash (check out strobist.com), you still need a flash in a lot of situations. Go for the Nikon SB600 (SB900 is overkill unless you get serious).
4) Tripod - depending on the type of photography you do, this has differing levels of use. I'd suggest a smaller travel tripod to start with, so you can get a feel for its use, then you can look at something bigger (more expensive). I'm happy with my Velbon MaxiL for traveling.
5) Polarizing filter and ND grad filters - these are pretty darn useful for landscape photography, but will put you out by quite a bit. I'd definitely hold of on these until you discover a passion for this type of photography. Saying that, the Cokin ND filters are good value if you really want these.
6) Camera bag - stick with something basic to start with as you will want to chose something later that better fits with your equipment and needs.
All in all, it's tempting to buy a lot of stuff, but your equipment will not make you a better photographer, experience will. Take your time to understand what your priorities are and then look at buying things to suit those, as your budget allows.