I would like to know which is a better (in performance) option :
I would like to run some light version of linux and do some very cpu intensive computations like Image/Video processing (maybe 3D later) and also process audio on them. Of-course all floating point mathematics.
Definitely #2, Pandaboard is an OMAP4 platform.
OMAP4 contains not only the ARM Cortex A9 (which is not likely to compete on it's own with dual core Atom), but, and this is crucial, a full C674x DSP core, both floating and fixed point mathematics.
The embedded DSP core in OMAP4 is fully capable of handling 1080p H.264 decode, with some resources to spare. I'm yet to see an Atom platform capable of that.
(shameless plug - my company is using OMAP3 and evaluating OMAP4 for some of our niche markets, and we might be interested in assisting in yours as well)