Hm, the only one I remember reading and really like was "Defiance". I also have fond memories about the first movie prequel, but I think, that like with the 2007 movie it's because "wow, something new, new backstory, new look, wow!" more than it actually being really good. After that I just lost interest, especially since movies weren't going to give a crap about those stories anyway.
I never liked stories set in present time. The past of movieverse Cybertron was much more interesting to me, and added something to the mythos, while those preset stories were just... there, not really doing anything for me. The worst one IMO is "Alliance", four issues about nothing.
EDIT: Ok, one exeption - I forgot about Reign of Starscream. That was pretty good, and that single Arcee "spotlight".