A couple of the hitters you mentioned are still working their way through freak wrist injuries that have to some extent, zapped their power (i.e. Derrek Lee, Rickie Weeks, Travis Hafner). Some figured to decline like J.D. Drew, Rolen, or Nomar, simply because they aren't really 40 HR sluggers year in, year out, but fall in that professional hitter mold with solid power more or less whereas others really did regress from a career-year type season (i.e. Jermaine Dye, Frank Thomas).
David Ortiz tends to be compared with Mo Vaughn as they have similar body types, but from what I can tell, he's more or less pulling the ball more for singles and doubles, increasing his BA but keeping the ball in the ballpark and therefore, the below-normal HR total. It could be his weight that's playing its part in nagging injuries. That and age, has probably slowed down Manny for much of the year as well.
As for Berkman, from what I know, he had a penchant for hitting groundballs at the outset of the year, but he's gone on little HR spurts accompanied by a drought here and there. Currently, he's been on a roll, which is encouraging though.
Wells, Swisher, Bay, and Andruw Jones tend to be streaky productive types and it seems like the power-less streaks have been more prolonged surprisingly. Beltran's nagging injuries affected his timing, but like the four mentioned, he figures to produce in bunches, much like the current spurt he's on.
As for Atkins, he just had a slow first few months this year, but regained his form as the Rockies' lineup collectively picked up steam. Zimmerman is too talented not to post good numbers, but the expectations probably should've tempered going into this year because the Nats became drastically less formidable an offense without Soriano at the top of the order.