The Nikon D3000 gets very mixed reviews, so I'd avoid.
The D5000 gets excellent reviews, though I believe that you pay a small premium for that fold-out screen. Could be useful mind, plus you get a great sensor, video recording etc.
Some useful comparisons here
You'll notice a lot of reviews mention that the D5000 doesn't have a built-in autofocus motor. This is an issue, but not a dealbreaker - all it means is that you'll have to autofocus with some, usually older lenses. If it bothers you that much (and it probably won't in practice), just stick to the newer lenses - there are hundreds available.
If you can afford it or see a good deal anywhere, I'd pay the extra for a D90, or even look for a gently used second hand model on eBay. The D90 is a definitely the best 'bang for buck' Nikon available, and I personally would be happy to buy second hand. My first DSLR (D40) was bought new and my current one (D2X) was second hand - it's like buying a car really, only for mileage read shutter count. Buying second hand meant I could get a low-mileage Mercedes for the price of a brand new Ford Focus, to stretch that analogy to breaking point
The Sony is great value for money, but has the slight
disadvantage of not having quite as many second hand lens etc. available for it. Not a massive deal, necessarily, and as Clyde says all the Minolta lenses work fine. I haven't used the Canon, but they're always good.