The Forces of Light and Dark in Ico
Constantly pursuing Ico and Yorda as they make their way around the fortress are the Spirits. These shadow-like creatures serve the Queen and are tasked with returning Yorda to captivity. They are weak enough that Ico can fight them and win, but there seems to be no limit to their numbers.
The origin of the spirits
There are two areas to examine when considering where the Spirits came from; who they are and what they are. I will start with the former. The biggest suggestion of the true identity of the Spirits is towards the end of the story, in the Casket Chamber. The Spirits Ico encounters here bear a striking resemblance to himself. As Ico destroys them one by one the caskets light up one by one, suggesting that each of the Spirits is somehow connected to one of the caskets. Since boys like Ico were sacrificed in each of the caskets, it is not a huge leap of logic to conclude a link between the Spirits and the boys who were sacrificed there. The obvious link is that they either are the other boys, or are some part of themselves they left behind after they died. There is further support for this idea in that the purpose of the sacrifice of the boys was very likely the activation of the Casket Chamber and destroying these Spirits seems to be the final step in doing this. Thus it seems the Spirits are in some way the sacrificed boys, and it is likely that the other Spirits in the fortress are also dead people.
Having determined in some general sense who the Spirits are, or were, the next thing to look at is what exactly they are. This is related to the nature of Dark Magic, as they are Dark Magic beings of some kind. Whether Dark Magic is actually magic or is more supernatural determines the nature of the Spirits. That is a separate topic related to all the magic in the story and how it all fits together, however it is the idea that the Spirits are dead people that suggests that Dark Magic is more supernatural than magical.
An important topic to consider is how the people who become Spirits do so, and why they do so. I mentioned in the section on the Casket Chamber that it is possible that being sacrificed in this manner is the common thread, but it in unlikely since there are a large number of Spirits throughout the fortress, and completion of the sacrifice seems to require the destruction of the Spirits anyway.
The types of spirits
Thus far I have only discussed the Spirits which chase Ico and Yorda around the fortress. The Queen and, for a time, Yorda are also Spirits, however their appearance and power suggest they are different in some way from the rest of the Spirits. This is why I often refer to them in particular as 'Dark Beings'.
While the Spirits which chase Ico and Yorda seem to be fairly simple creatures, relying on physical strength to complete their task, the Queen at least commands some impressive powers. It is in this that the two types of Spirits are truly set apart. The ease with which Ico dispatches the Spirits throughout the fortress suggests that, if they truly are something left behind by the dead, they are a remnant weakly hanging on to existence. Despite some interesting abilities, such as flight and the use of the portals, they could actually be considered an inferior form to that of a living person. The Queen on the other hand is indisputably a far more powerful being than normal people, and rather than hanging on to existence she is actually far stronger than those who are still alive. Rather than simply being a person in another form, or a remnant of a person, she has become something more.
The basic difference between the two types of Spirits seems to be what part of the original person they are. Exactly how the Spirits throughout the Fortress relate to the people they apparently came from is unknown. They might not even be related to the original people in anything other than physical appearance. They do not seem to have distinct personalities or a will of their own. When Yorda becomes a Spirit she seems to be the same person, only in a different form, and the Queen is quite obviously a complete person. The Queen and Yorda seem to truly be dead people brought back in another form, whereas the other Spirits, while related, seem to be something else.