David Frampton has an interesting idea for how to display non-universal iPhone apps on the iPad: put a black border around them, much like how iPhone apps will display if they are not scaled-up.
I think it's a brilliant idea. It makes them distinguishable, but at the same time seems not too obvious.
If you look at iPhone apps on the iPad today, you may be able to tell the difference between the 57x57 pixel icons for iPhone apps versus 72x72 for native/universal iPad apps.
Would Apple ever consider doing something like this? Hard to say. Initially Apple has wanted to make it clear that iPhone apps are available for the iPad, but nearly everyone I've heard who has run iPhone apps scaled up on the iPad says that the experience is definitely sub-par.
When iPhone OS 4 comes to the iPad this fall, perhaps one of the ways that Apple will try to nudge developers towards producing either universal apps or iPad versions will be to scale their icons. I'm reminded of the way that System Preferences in Snow Leopard handles 32-bit Preference Panes: they force the user to re-open System Preferences. It's not a huge issue, but just enough that I can imagine developers wanting to avoid the "ugh" factor.
The biggest reason that I see in favor of doing something like this is that there's very little downside. The icons will look better not being scaled up and it helps the user identify iPhone applications at a glance. Developers would have a slight motivational push to make iPad/universal versions of their apps.