Eriu is one of the closest nations to being good, as the Sidhe and a few lingering Tuatha have volunteered to return and aid their conquerors in the wider world. Generally water-magic or nature based nations are more closely aligned to being on the side of "good" than "evil"; Pangaea is not so much evil or good but amoral, emotional, and animalistic. The nations of Tir Na N'Og aren't really all that bad despite a warlike past, as they celebrate art and poetry as much as war. The Tuatha/Fir Bolg are a much less warlike version of the Van of Vanheim, and are more quickly banished and defeated (whether ironic or intentional, i also have a much harder time making Tir or Eriu work in-game than any of the much more effective Van nations.)
Of the three subsea nations, Oceania is by far the least sinister. Atlantis is strange and monstrous, but Ryleh is of course evil and alien.
Tien Chi is probably a reasonably good empire; it's failings are ones of external conquest, but it's underpinnings of the "way" remain.
Ulm and Marverni aren't so much good but proud half-civilized marginal nations. Marverni sort of wishes they could commit atrocities but aren't particularly good at them.
Man could be considered good if you don't think too hard about their past
. But as a feudal nation they're good only in the broadest sense of the word.
Pythium and Arco are probably a good nation insofar as an Empires can be considered good. Marignon gives in to the fear of death and makes pact with the "lesser" evil; Ulm is somehow corrupted (the nature of the "Night of Treason" isn't explained or foreshadowed much in 2nd age Ulm) and becomes a dark shadow of it's former stern self.