I am actually in the same process of comparison right now...

The HD2 is a more mature device with more apps and and more complete, albeit annoying, operating system. I already have an N900, coming from (gulp) an N97.

HTC did wonders with its SENSE interface for the UI. Still, certain parts of the OS are not finger-friendly and were designed for a Stylus, which you cannot of course use with this phone. Anyway, two things made kill my decision to get the phone, other than spending too much cash on going from N97 to N900 then HD2!:

1- Camera on the HTC is horrendous! Images are fuzzy, and quite frankly look like a VGA camera. Whereas the camera on the N900 lacks the colour warmth of the N97 and the N95 8GB (the master of all phones) [probably because the N900 uses a warmer palette for the screen display, so images are perhaps taken less warmly so that they look right on the display?]
2- No confirmed update to Windows Mobile 7 until now (Meego anyone *sigh*), and the HD3 is to be released in November, effectively killing the HD2 to a certain extent. I dont wanna get a phone to keep changing.

My advice is: wait 1-3 more months, or get something running Android. Sad to say: Nokia is horrible in maintaining its OSs, and is keeping everyone in the dark about Meego and Maemo. Android is a more mature OS with tons of apps, and it is also Linux-based, allowing a degree of hacking for the hacking-interested.

Can't find my N900 stylus for the past 2 hours!