Why did he command to kill the entire city of Nov?
Malbim: This was so people will hear and fear, and not support David.
Why did he command to kill even the animals?
Radak (citing Yuma 22b): When Sha'ul and the nation spared the animals of Amalek, a Bas Kol (voice from Heaven) said "Al Tehi Tzadik Harbeh" (Koheles 7:16)! When he commanded to kill even the animals of Nov, a Bas Kol said "Al Tirsha Harbeh" (Koheles 7:17)! Me'iri (22b) - one who is merciful in a place proper for cruelty (against Resha'im who should be killed), that mercy is turned to cruelty on others. His 'advocate' becomes his prosecution!
Why is Nov not listed among Sha'ul's sins? Even "Beis ha'Damim" (2:21:1) refers only to the Giv'onim that he 'killed' through this (their income was via the Kohanim)!
Radak: The Kohanim were liable. The Navi did not reveal their sin, other than that of Beis Eli. Even so, Sha'ul was punished for their blood; Pelishtim killed him and his three sons.
Brachos 12b: We learn from Sha'ul that anyone who is embarrassed for his sin, all his are forgiven. "v'Lo Anani Od Gam b'Yad ha'Nevi'im Gam ba'Chalamos" (28:15) -- he did not mention the Urim v'Tumim, for he was ashamed that he killed the Kohanim in Nov. 1 (It is omitted, for it turned into a merit, i.e. pardon of all his sins. What 'list' of Aveiros does Radak discuss? Verse 28:18 mentions his sin(s) for which his kingship was removed! - PF).
R. Yochanan (12b): We know that his sins were pardoned, for Shmuel told him, "u'Machar Atah u'Vanecha Imi" (28:19) -- you will be in my place (in Gan Eden, surely, one of the highest rewards there is!). Rabanan learn from "v'Hoka'anum
