Forgive me for being ignorant on this because I'm a novice on alot of what you all talk about, as it shows repeatedly. lol
I understand IQ is the same and probably would be for the D5000 as well. But when I see pictures taken with these (Nikon Website), there is a huge difference in clarity amongst all three of them. I'm sure the lens they're using is a factor in the quality of the pictures but few of those pictures are taken with the high dollar lenes. Maybe this is where my confusion comes from?
You will definitely notice a difference between a gen 1 entry level Nikon and the gen 2 mid-range and semi pro models.
Having cleared that up, pretty much as soap said, you will not see a difference in IQ between your two choices. The controls are placed differently and the build quality is also different. One of the biggest differences is the AF system. The multi-cam 3500 (D300s) is far superior to the aging multi-cam 1000 (D90). The D300s's AF is faster and more accurate. Trust me, I have both. Either way you will definitely see a difference over the D60's AF system for sure.
Basically both the D90 and D300s are great choices. It comes down to how much you want to spend and if you want to buy more lenses as well. Although, if you want to stay in the FL you're in it may cost you a lot more. The lens you have is a good lens all the same.