I remember doing a hex cell once (as part of a hex maze), I found that using 3 dimensions made my problem a lot easier than two, even though we are working only in 2d.

Imagine vectors I = (1,0), J = (1/2,sqrt(3)/2) and K = (-1/2, sqrt(3)/2), which is really unit vectors at 0, 60 and 120 degrees. Every center of a hex is identified by three integers (a,b,c) which correspond to the 2d coordinates aI+bJ+cK. To find the six neighbors of (a,b,c), just add or subtract one from any of the a, b or c.

I was surprised but using this system made my code a lot easier to understand, and write.