I've got a few, though some don't really 'make' FMA:
- Roy Mustang's quote: "Oh... It's raining" ... "No. It's raining."
- When Ed goes to show the Fuhrer how dangerous the 'qualifying ceremony' is, only to find his own spear cut down by the Fuhrer's sword.
- When a civilian asks Hohenheim "What are you?". Hohenheim replies "A monster". On the same page he says that are frames with Hohenheim, Bradley, Gluttony and others. coooooolness
Hmmm... Ed talking down to Rosé in the first chapter was always a favourite of mine. Particular quotes escape me, but any manga that bad-mouths religion that early on instantly grabs my attention.
Izumi breaking into Greed's hideout! A personal favourite. "Who are you?!" "I'm a housewife!" Then Ed kicks Greed's ass, which I also enjoyed. In fact, that whole arc, with Wrath and the soldiers massacring the chimeras, was an important one for me. Made me sit up and think "Hey... This isn't normal." Martel dying makes me cry to this day.
Greed's death, still laughing, had a pretty big impact. And Lust being killed by Roy... Anytime that the brothers end up fighting Scar, particularly when Winry turned up that time, and Ed told her that she was meant to restore life, not to kill...
And yeah, the Ishbal flashbacks were exceedingly well-written. So all of those, probably.