Google will consider all the links from one domain but be aware, if you have a lot of links from the respective domain is posible that Google cosider that the links have not built natural and in this case your site will be put at the end of the index list
It really is interesting... Google does have its own unique way to even change their already unique algorithm. But you will be on top frankly if your site does have unique content which was published no where else but only in yours.
Esentially google makes minute changes across multiple datacentres, finds which change lead to the best results and combine the ones from the most high performing datacentres.
Google will devaluate your links from the same domain: but if you use unique anchors on every page - the links will not be considered sitewide and will caryy a higher value
So a little php script for the bottom of each page to insert different anchor text linking back to the home page. :: thinks about it a bit ::