You know, come to think of it pretty much every FF - even those with a lot of lighthearted elements - are pretty dark. FF7 had a lot of dark moments, for example. Remember the attempted live execution of Tifa? Shinra's experimentation? The effects of Mako energy? Aeris' fate? Biggs, Wedge and Jessie? Marlene being used as leverage by Cait Sith?

FF6, FF9 and FF12 also had many dark moments. FF Tactics did as well - though that's already been brought up.