Having not heard either of the bonus-tracks yet, it comes down to a duel between Inside the Particle Storm and The Mundane and the Magic - both are very strong songs with unparalleled originality.
Icipher was my first favorite of the album, but the aforementioned two have passed it by. Misery's Crown, The Lesser Faith and Nothing to No One are very high on my list as well.
Actually, the only songs that don't stand out from the album are Empty Me and Focus Shift, and that's simply because they are squeezed between such masterpieces as ItPS, MC and TMatM - they compliment the whole album very well, but don't stand out as much.
In the end, Inside the Particle Storm it shall be for now.
-Villain