Top 5? How about Top 5, in three categories?
The App Store has 20 categories for Apps, it is impossible to determine the best 5 apps overall, considering the large amount of diversity and uses. There must be categories to compare objectively and I have narrowed it down to three; Utilities, Navigation, and Games.
My Top 5 Utilities:
LogMeIn Ignition
Simplify Music 2
Rowmote Pro
iRetouch
Pandora
My Top 5 Navigation:
G-Park
Mapquest 4 Mobile
Navmii
Navigon
Motion X GPS
(I have tried many GPS apps but I only have G-Park, M4M and Navmii for UK installed, I impatiently await the US release of Navmii)
Top 5 Games:
EliminatePro
JetCarStunts
Red Bull FMX
Topple
Tiger Woods
These 15 apps will surely get you where you are going, entertain you, and allow your iPhone to do some amazing stuff, like remotely view and control your computer!