wmpoweruser has an excellent video comparing these two phones. What’s striking is that the HD2, while it has a substantially larger screen (4.3” vs. 3.5”), doesn’t seem to be much larger or heavier than the iPhone 3GS, and indeed is thinner.
The two devices have a number of common features (e.g., Bluetooth, WiFi, GPS). However, the HD2 has more firepower; a much faster processor (1GHz vs. 600MHz) and substantially more memory. The HD2 also has removable storage (the iPhone doesn’t), a removable battery (ditto), camera flash (ditto), and a more powerful cameral (5MP vs. 3MP). The video’s conclusion: the iPhone 3GS is good, but the HD2 is better.
wmpoweruser is a Windows Mobile site. Nevertheless, the video seems reasonably objective, and is an interesting and entertaining 5 minutes.
The HD2 does have an Achilles heel; the rather anemic Windows Mobile OS. Version 6.5 is only an incremental improvement over 6.1. HTC Sense hides WinMo UI issues, but it’s sort of like putting lipstick on a pig. With version 7 still at least months away, the WinMo OS drives some towards the iPhone. In this regard, see Is Windows Mobile’s Death Exaggerated? I bought an iPhone 3GS.