Some stories are (way) more worth counting than others. I find many are just not worth it. Dead to Rights (Batman Confid), Journey Into Knight, Rules of Engagement, even Terror arguably are just not worth it for me. I know I'm not the only one who doesn't count those.
My core are:
Year One/Shaman/The Man Who Falls (Man Who Falls reprinted in Batman Begins:The Movie & Other Tales of the Dark Knight TPB)
Her Sister's Keeper
Monster Men
Mad Monk
The Man Who Laughs (here, b/c Mad Monk's ending refers to the MWL's beginning)
Prey
Four of a Kind
Gothic/Venom/Going Sane/Blades....some uncertain order
Long Halloween
DarkVictory, etc