I was wondering what the connection between Wesir and the Apis Bull are. I know that it was used as a kind of omen and was held in high regard, but why is it linked so closely to Wesir? Traditionally, I thought that the Apis Bull was only related to Ptah. What does the Sokar aspect have in relation to the Apis Bull outside of Wesir? 

Seker's name is hard to define, and he does not have too may writings on him; or that he appears in. He does however appear in the Book of the Dead and the Pyramid Texts, though he is usually always linked with Usir or Ptah: or all three as Ptah-Seker-Usir. He is sometimes thought to be linked or associated with re-birth or resurrection. This is probably one of the leading factors as to why he is linked to Usir or Ptah. Also, sometimes Seker is noted as being a craftsmen of silver, producing silver bowls?, and this links him to the great craftsman Ptah.

With Apis, he was highly worshiped in the Ptah cult. It was believed that Apis's mother was a virgin and was impregnated by Ptah himself: thus Apis is his son. I suppose with the cult of Ptah in Men-Nefer having links to the Usir cult Apis becomes seemingly connected to Usir. Bulls along with cows were also used to pull plows for farming, so I would imagine this linked the animals to Usir, lord of agriculture. Seeing as each spring the new growth on the fields was seen as a 're-birth' of the plants from the previous year, Usir-Seker becomes linked to all this as well.

As far as my knowledge goes, the Apis bull wasn't considered the son of a god, but an incarnation of a god when it appears with certain markings symbolizing luck and good omens.

The LAGG lists a syncretized form Ptah-Sokar-Osiris-Apis, which has been found in a Hotep-Di-Nisut formula in the Serapeum.

And it lists a Ptah-Sokar-Apis-Osiris, found in the Serapeum as well.

But I think that in both cases Apis is connected to Osiris as either Apis-Osiris or Osiris-Apis

and there is one record found on an ushabti of the Apis bull which mentions Apis-Sokar-Osiris

"The Complete Gods and Goddesses of Ancient Egypt" section on Apis (pg 170-172):

After his death Apis fused with Osiris, becoming the composite god Apis-Osiris or Osirapis (and later, in Hellenistic times, the anthropomorphically depicted god Serapis). In this context the living Apis bull itself was sometimes called the ba of Osiris, and the process of assimilation with other deities also led to the composite Osiris-Apis-Atum-Horus. In some funerary texts, Apis was said to thresh the grain in the afterlife, but it is usually his power and virility which are tied to the deceased -- so that in the Pyramid Texts the deceased king claims the surging power of the bull's phallus as one of the ways in which he is said to be able to rise up to the heavens (PT 1313).

found in the Serapeum: "Oh Apis-Sokar, great god, Lord of the Shetayet-shrine, I have come, I am the Sem priest and king's son!"

Hart's Dictionary entry on Sokar provides the following, which might be of interest:

 From the Old Kingdom Sokar was seen as a manifestation of Osiris slain by SETH in Nedyet...Equally possible, however, is an explanation of the god’s name connecting him with a ritual of the fertility of the earth: SESHAT in the temple of Sety I at Abydos calls Sokar ‘cutter’, from his holding the mattock to break into the first clod of Nile silt...In the Pyramid Age Sokar is manufacturer of the royal bones and in the Book of the Dead he fashions the silver bowls for the idea of moulding objects as an artisan Sokar becomes associated with the mixing of aromatic substances to provide the unguents so important in Egyptian ritual. His craftsman image made the identification with Ptah, also a god of artisans, occur as a smooth transition. As Sokar of ‘Rosetau’ or ‘mouth of the passages’ (i.e. into the Underworld) he was the patron deity of the necropolis to the west of Memphis. He is ‘lord of the mysterious region’ and is prominent in the decoration of Theban royal tombs. This emphasises him, like Osiris, as a resurrected god of the dead, of unrestricted movement and power as his epithet  'great god with his two wings opened’ indicates.

Hart (as does Wilkinson) also talks about how the Apis bull is linked to the king, and just as the king becomes Wsir at death, according to the Pyramid Texts, so too, according to Hart, does the Apis bull become Wesir.