Very few enemies have significant resistance to spirit damage (or electrical damage). For the most part, you can rely on both throughout the game.
By contrast, many enemies have some resistance to nature damage. Undead, constructs and so forth are totally immune to nature damage, and even basic darkspawn have some resistance. Nature damage should not generally be relied upon as a primary source of damage, although it can be situationally useful.
Bear in mind that spells like stonefist actually do physical damage, so I think the only spell which deals nature damage is stinging swarm, so basically don't rely on stinging swarm (although you can certainly use it, it does pretty good damage).
There is one exception to this, the final boss of the game is highly, highly resistant to all forms of elemental damage apart from nature damage (but including spirit damage). Said final boss also deals very high spirit damage, although there is an item you can obtain shortly before fighting it which grants very high spirit resistance.
In terms of resistances, all forms of damage are encountered throughout the game. Fire, nature and spirit are probably the most common. Generally, it's pretty common sense. Rage demons and dragons will inflict fire damage, spiders will inflict nature damage, enemies like arcane horrors tend to inflict spirit damage and mages will inflict damage using whatever spells they have (NPC mages tend to use fire spells). Due to the power of the latter, probably the best form of resistance if you have a choice is actually magic resistance, which also has no cap (it's possible to be 100% magic resistant, at which point no hostile spells will affect you).
