The attack on Kells. So much. Seeing Abbot Cellach struck down, after it'd been shown that he was the strongest out of all the people there. Not to mention the collapse of the scaffolding...
You only see the top of Crom's cave from the outside in a shot or two—it seems to have a spiky design on it. According to the DVD Commentary... it's the blood of Crom Cruach's human sacrifices.
The Vikings in general. Huge, hulking figures with glowing red eyes that speak a guttural, growling language.
This movie does not gloss over the destructiveness of the Viking raiders, and while most actual deaths happen offscreen, it makes it painfully clear that an incredible number of people were killed. Crom Cruach is also quite likely to scare the pants off unsuspecting viewers.
Brendan and Aidan having to leave the Abbot behind to die because there's nothing they can do to save him.