<p>I'm developing a performance critical application for Intel Atom processor.</p>

<p>What are the best gcc optimization flags for this CPU?</p>

There is a cool framework called
Acovea (Analysis of Compiler Options via Evolutionary Algorithm)
, by Scott Rober Ladd, one of the GCC hackers. It's a genetic/evolutionary algorithm framework that tries to optimize GCC optimization flags for a specific piece of code via natural selection.
It works something like this: you write a little piece of benchmark code (it
really
has to be little, because it will be re-compiled and executed several thousand times) that represents the performance characteristics of the larger program you want to optimize. Then Acovea randomly constructs some dozens of different GCC commandlines and compiles and runs your benchmark with each of them. The best of these commandlines are then allowed to "mate" and "breed" new "children" which (hopefully) inherit the best "genes" from their "parents". This process is repeated for a couple dozen "generations", until a stable set of commandline flags emerges.