Mother Russia has always been my favorite.
My problem with 'in the beginning' and 'mother russia' ...well not problem really...but they've got ridiculously high body counts. And mother russia was just borderline unbelievable....
No really. I put valley forge, just cuz the bits of the book get so emotional and it's really just Ennis summing up what he's said with the whole series. Like they gave peter jackson the oscar for 'return of the king' it was really for the trilogy. Also Valley Forge parallells with Born really nicely rounding off the whole thing.
Man of Stone and Black is White are really perhaps the best stories, but they don't stand alone as well as say Slavers or Tyger or the Cell. Also barracuda arcs aren't really as complex, but have some really good dialogue and character.
I like them all.
Edit: and this is so the poll I've been waiting for.