As my first DSLR I purchased the D5000 with the 18-200 lens. I figured the D90 was much more advanced and I didn't need the added features.
I love my camera, and I have taken many pictures that I am very happy with. I still have a lot to learn and grow though..... However, I wish I would have understood the in-body focus motor. As others have said, there are many lenses you will want that don't have the AF-S. You will be forced to spend much more money for a lens that has a built in motor.
I find the tilting LCD helpful at times, but most of the time, I frame with the viewfinder. From what I understand, they both have a version of the same sensor, so picture quality is similar.
The D90 has more focus points, and should focus faster with all types of lenses. I believe it may also have a commander mode for off camera flashes (something I am going to look into next). There is also a depth of field preview button and more direct control of camera settings with dedicated buttons, switches, etc.
Overall, I am not looking to upgrade my body at this time. I can still grow with what I have. I am no professional, just like to have fun on the weekends with my camera. The D5000 is a great camera, but if I had to do it all over again, I would probably get the D90. Hope this helps. Both are great cameras. Get something and start shooting and enjoy the sport, and worry less about the equipment.
-Andy