UPDATE
As of more recent versions of iOS, you can only attach the profiler to your own developer-signed apps.
ORIGINAL
Using Xcode 4.4.1 and my iPad 3 running iOS 5.1.1, I'm able to use the Core Animation and Time Profiler instruments on third-party apps. I tried it with Twitter and Minecraft PE.
The profiles are rather useless since I don't have symbols for the apps. I just get a lot of addresses in hex. And Instruments won't even show me the disassembly of the apps. I believe this is because iOS, for security, doesn't allow Instruments (or gdb
or lldb
) to look at the address space of apps installed from the App Store.