They are a unique category of fields commonly referred to as standard lookup fields. Unlike custom lookup fields, they have the generally have the "cascade deletion" property set to true, and unlike custom master-detail fields, they may have the "always required" property set to false. Also, these fields can restrict deletion of accounts when certain conditions are met. To learn their special properties, refer to Help for any particular field.
EDIT:
It's now possible to enable custom lookup cascade deletion, which has a similar behavior to how Accounts/Contacts, Account/Cases, and Account/Opportunities behave, but without the ability to restrict deletion when certain criteria are met. You can read this Knowledge Article for more information.