You can just use the iPod/iPhone defaults in Compressor 3 – they should automatically letterbox your HD footage or there is an option to anamorph the shots – if it isn’t happening change the manually set it. This is what I have been doing the last few days (NB my footage is either widescreen PAL (576/50i) or 1080/50i)
Copied the H.264 for iPod video and iPhone 640×480 (found under Apple > Apple Devices)
Changed “Device” to iPhone (Local/WiFi)
Changed “Aspect Ratio” to 16:9 (480×270)
Changed “Frame Rate” to 25
This is giving me really good results and the beauty is the iPhone screen is 480×320 so it is basically a native format for the screen without the need to up or down scale. You do get black bars top and bottom as the iPhone screen is 3:2 (1.5:1) not 16:9 (1.77:1) but there should be no stretching.
Hope this helps.