I think that the issue with the iPad and "HD" apps is, despite the HD name, more to do with screen size than resolution. Because the iPad has so much more screen area than the iPhone it means that developers have the space to develop totally different user interfaces for their iPad versions and some have chosen to charge extra for this and others (the ones who made universal apps) haven't.
The iPhone 4 still has the same screen size so you'll see sharper detail on the screen but no total UI redesigns so I wouldn't expect any app vendors to try and charge a different fee between iPhone 3 and 4.
A lot of what you see on screen, e.g. Text and standard Apple user interface elements like buttons and wheel selectors, are actually rendered by the operating system and not directly by the application so it will all automatically look sharper when you run exactly the same app on the 4 vs. The 3GS; the app developer didn't need to change anything to give you that extra sharpness for those elements, only their own graphics, so it would be outrageous to charge for a separate version and the market and reviews would crucify them for it.
- Julian