As of now.
1. Nexus one
1.01 HTC Desire
2. Soon to be launched iPhone 4
3. Samsung Galaxy S
4. Motorola Milestone / Droid
5. HTC HD2
N1 and desire are same phone to be honest. Desire scored over N1 with FM and SenseUI, but has other limitations like slightly difficult root method and as of now you cant permanently flash Recovery on it (though paul made it easy just today). And as Nexus is Google branded it will get the updates first and faster than HTC or anyone for that matter. And you can always get the Sense port on N1.
iPhone 4, mostly because of same boring UI is not my top pick. 3GS wont feature in my list at all, but iPhone 4 deserves place there.
Galaxy S will set the benchmark for the hardware, but I hope they make serious changes to TouchWiz UI and it comes from samsung, they product fantastic phones but do not back them with updates over time like HTC or apple or google does. They gotta change that attitude. And the plastic quality is not that great from the initial impressions of people. But TWUI needs to improve more.
Then Milestone is best Android phone for people looking for hardware QWERTY.
And HD2 with all its almighty screen & thanks to HTC makeup over WM.
No X10 as at this point I am coming off 1 frustrating week with X10 and its stupid buggy software causing me some headaches.