At this time the best choice is desire not nexus. Google had already confirm no more production of nexus. Google CEO said the nexus was just an experiment from google to show Android can be a equal if not better alternative to the iPhone. All google partners htc, SAMSUNG, motorola will develop the phones. The nexus will still be used by google to improve the android platform. Those having nexus will definitely get software upgrade faster, eg my nexus already updated to froyor 2.2 a month ago while desire will have it end aug/sep, motorola sep, Sony in dec, SAMSUNG by oct etc.
The desire has local sis warranty, extra ram 576mb versus nexus 512mb, and I feel it's hardware keys is better than nexus soft keys. Performance wise not much difference as both are same specs basically and hardware chip and graphics. For those who are new, nexus is actually a htc product make for google. The desire is htc version of the nexus.
If you like to tinker with rooms, the nexus offer you more options. This might change later once there are more desire users.
As a smartphone you won't go wrong buying either one. It is just like asking to buy city or vois, accord or camry etc.
But I would say the trackball in nexus is damn good, don't know why desire didn't follow. Maybe htc wants the desire to be more different. I can now set different colors to miss call, SMS, tweeter and google mail, other email - very useful. When silent mode, I just look at the trackball and I know what is incoming