I have some brief questions about the Elder Scrolls in terms of magic.

It is basically considered illegal to capture the souls of humans and elves, correct?

If so, why can you capture the souls of ghosts? Aren't ghosts essentially disembodied spirits.

Also, how can you capture the souls of skeletons?

This debate comes up a lot around here, and usually comes around to the definition of a soul, and whether the ghosts and skeletons are actually the spirits of dead people or some other form of energy is used to animate them. Another theory is that it's all game mechanics.

I personally feel like the energy that's used to animate a ghost or skeleton isn't an actual person's soul, usually. When a Wraith or a Ghost is left behind, it's not the entire soul but an angry and malcontent portion of it. Game mechanics conflicts with this, though, since there's a Wraith in Knights of the Nine whom can be killed and soultrapped, and yet his spirit appears, cleansed, in the Priory soon afterwards.

Liches present another problem...they never really died, and still have their soul, but can be soul trapped. Perhaps their blasphemy caused Arkay's protection to abandon them. However, Vampire NPCs can't be soul trapped in either Morrowind or Oblivion, implying that despite their perverse existence, Arkay hasn't abandoned them. I would call this a game mechanic purely. I think Arkay abandons any entity which makes perverse and unnatural attempts to extend their life. Creatues like werewolves, vampires and liches are no longer human/elf/beast person.

Mechanics aside, I find the idea of capturing the "animating energies" of undead to be plausible. This can explain why essentially golem-like entities such as skeletons can be soul-trapped, and why ghosts and liches can be captured without actually taking the "soul" as it where.

I have another question. Daedra cannot actually be killed, their souls return to Oblivion to get new forms. Would it be theoretically possible to soul-trap every single Daedra?

It should be theoretically possible, as daedric armor is an armor which contains the soul of a daedroth.

About Arkay, I though (because I read it in a book-ingame ) that only bodies that receive proper funeral rites are protected by his law...
So you should really be able to capture vampires' souls, or npcs', for that matter. Its just simple game mechanics.

It's gameplay mechanics (Oblivion's mostly) that just trap the energy. As far as the lore is concerned you trap the whole personality.

There are a few more examples but the Soulgem with the Soul of Prince Ator in Redgaurd and Feyfolken make it really clear.

I don't know through what magicks, but Nords have a tongue fettish, where conquering Nords will remove the tongues of their enemies and sew them together, to make totems of a kind. Each tongue ligament is enchanted to retain the voice, or spirit, of the fallen and give them strength in battle. Pretty cool soul trapping, that is. Thought I would mention it...

Another vote to the game mechanics pile. Basically, there are two kinds of actors from the engine's perspective: NPCs (things with dialogue and morphable faces) and creatures (things without dialogue and morphable faces.) NPC souls require black soul gems and creatures go in regular soul gems. That's why a human ghost goes in a regular gem despite being a human soul and a dremora goes in a black gem despite being a daedra.

Souls are a mystery because those who delve into figuring them out tend to zero-sum. Although I've wondered if the soultrapping/recharging/enchanting process could be reversed to create souls.