I don't know if GCC has any Atom-specific optimization flags yet, but the Atom core is supposed to be very similar to the original Pentium, with the very significant addition of the MMX/SSE/SSE2/SSE3/SSSE3 instruction sets. Of course, these only make a significant difference if your code is floating-point or DSP-heavy.
Perhaps you could try:
gcc -O2 -march=pentium -mmmx -msse -msse2 -msse3 -mssse3 -mfpmath=sse
