Dunno, that was my initial thoughts too.
HTC Desire has Sense, which while annoying is better than nothing. N1 has car mode. HTC suck at updates on the desire. N1 has trackball. N1 is thinner. Desire has slightly more memory.
Having had both of them I can tell you exactly the differences. [I sold my Desire to my mate and use my Nexus]
1) The Nexus has dock pins on the bottom of the phone for the desktop cradle and car dock, while the Desire docks/cradles rely on connecting the usb connector.
2) The nexus is quad band while the desire is "only" triband
3) The desire has a FM radio. (the nexus has the hardware, but not the software, there have been some hacked roms that attempt to enable the functionality but they are all a bit buggy IIRC)
4) The Nexus has a noise cancelling mic on the back
5) The desire uses HTC's sense UI overlay while the Nexus uses straight stock android, so the nexus will always get the android updates first (especially as its now also "Google Dev Phone 3") [I actually really like sense and when it's properly hacked to the Nexus under FroYo will be installing it]
6) The HTC's IME keyboard implementation is far superior to the stock android one (at the most basic level because you can use a long press on the letters to get symbols, while on stock you have to select the symbol keyboard) [this is easily transferable over to any android phone though, i run HTC IME on my nexus with no issues at all].
7) Widgets - The Desires widgets (which are technically part of sense) are much better than stock. i.e. Friendstream, the calender, the Music player one.
8) Homescreen buttons - On the desire they are actual physical buttons, while on the nexus they are touch sensitive areas at the bottom of the screen
9) Every man and his dog appears to be getting a Desire, Nexus therefore rock :rasp: