Design ( outer appearance, build quality, etc )
The main thing here is the 3.5-inch screen of the iPhone vs the 4.3 inches of the HD2. Both displays offer good image quality indoors, but the iPhone has the upper hand outdoors, in bright sunlight.

User Interface
HTC Sense UI consists of multiple tabs that will allow you to quickly get to almost any function of the phone it adds integration to Facebook, Twitter and YouTube to the mail UI. Apple’s UI for the iPhone is simple and has a user-friendly interface.

Messaging
The HD2 comes with dedicated Mail tab that allows users to go over shorter versions of their emails on the fly. Its advantage is the ability to instantaneously switch between email accounts which is missing in the iPhone.

3rd party Software
Apple is the clear winner here with many apps that Windows Mobile users can only dream of getting ( may be one day with WM7 ). The iPhone apps are also less expensive when compared to the uber expensive WM apps.

Camera
The HTC HD2 sports 5-megapixel camera, while the Apple iPhone 3GS comes with just 3-megapixel one. Moreover, the HD2 is equipped with a flash, which makes it the better “cameraphone” of the two. But some HD2 device has some issues with the camera.Both handsets capture videos at 640×320 pixels and 30 frames per second.

Multimedia
HTC comes on top once again, thanks to its 4.3-inch screen and with 3rd party app like Core Player it supports a lot more format than the iPhone.

Internet
The superior screen of the HD2 comes to its aid one again. With 3rd party browsers like Opera Mobile / Skyfire. the HD2 can even play flash animation which is a no go for the iPhone.

Call quality
Both the handsets fail miserably when it comes to in-call quality

Battery
Not the selling point for both the devices.