Apple finally finished making changes in App Store; as the result, the iPad apps were separated from the iPhone apps.
This decision was logical as everybody has been waiting for this and it happened. Now, opening App Store through the iTunes we can see the switch on the top: 
Choosing necessary category we sort out the apps for our device.
At first Apple probably decided to distinguish the iPad-specific applications just by adding HD to the app name but even they underestimated the number of developers interested in this platform. Majority of these apps will easily be lost in abundance of various programs and games that is why this separation took place.
John Gruber, one of the most authoritative and quoted Mac community bloggers wrote in his twitter:
Running iPhone apps on your iPad is like driving your new BMW on the sidewalk.
And we can’t disagree with him as the iPad has considerably larger screen and ought to play its own applications instead of stretching the iPhone apps!