Having shot with the D90 and the D5000, I also feel the D90 is the better choice if you can afford the additional cost up front. If not, buy the D5000 and have fun, it's not a *bad* choice.
After more than 10 years on hiatus from SLR ownership, I started with a D60, which the D5000 is in many ways a 'replacement' for. After a few months, I bought a D90. The D90 had crossed my thoughts when I got the D60, but I decided to save a few bucks. After shooting with the D90 for about 2 years, I decided to get a D700.
D90 has a slightly larger LCD. That is good if your vision is not. However, it doesn't move around and tilt like the D5000.
The D90 meters and focuses with many more lenses than the D5000 does, which is good if you already have some lenses from shooting film, or you are likely to find some somehow.
With my D700 purchase, I also picked up the 24-70 2.8 and a 70-200 2.8 VRII, and those lenses have the silent wave motor built in to them, and they will work fine on a D5000 - and they are 2 of the 'top' Nikon pro lenses at this time - so don't think that you are limited by a D5000.
D90 has a better battery than D5000, the EN-EL3E as opposed to the EN-EL9.
D90 has the 'commander' remote flash control built in if that is important to you, D5000 does not.
Now, a buddy has a D5000, which is why I've had the opportunity to play with it a bit. He gets amazing pictures out of it. He has a great eye. As a technical shooter, he isn't there yet - but he is improving every day with some coaching.
The best photographer with the worst equipment makes great images, while the worst photographer with the best equipment does not. Never forget this.