Storing and querying datasets that contain objects in a geometric space have always required special treatment. The choice of data structures and query algorithms can easily make the different between a query that runs in seconds or in days. Much of the fundamental work has been done in the late eighties and early nineties, for examples around topological relations (disjoint, meet, equal, overlap, contains, etc.), direction relations (north, north-east, etc.) and distance relations (far, near), and also with respect to spatial data structures (a great survey by Hanan Samet).
With location becoming a more important attribute to many modern datasets a solid understanding of the tradeoffs is important. In 1994 Ralf Güting wrote an overview of the state of the art for a regular databases audience in a special issue on Spatial Database Systems of the VLDB Journal. It is an extensive but relatively easy read and gives a great introduction to the back-to-basics of Spatial Database Systems.
An Introduction to Spatial Database Systems, Ralf Hartmut Güting, The International Journal on Very Large Data Bases - Special Issues on Spatial Database Systems, Volume 3 Issue 4, October 1994, Pages 357-399