It was originally designed by Bramante in the form a huge equal sided Greek Cross topped by massive circular dome based on the Roman Pantheon. It was to be a merging of traditional Renaissance church styling (layed out like a cross, oriented on the compass rose, etc.) with Roman temple styles (large domes, columns, etc). It was intended to be extremely innovative with regards to the central dome, as the dome would be supported by four large piers rather than be perched on top of a supportive circular wall such was used in the Pantheon.

Raphael then modified these plans to include
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"the nave of five bays, with a row of complex apsidal chapels off the aisles on either side."
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After Raphael's death, Michelangelo took over as architect and:
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"blurred the definition of the geometry by making the external masonry of massive proportions and filling in every corner with a small vestry or stairwell. The effect created is of a continuous wall-surface that is folded or fractured at different angles, but lacks the right-angles which usually define change of direction at the corners of a building. This exterior is surrounded by a giant order of Corinthian pilasters all set at slightly different angles to each other, in keeping with the ever-changing angles of the wall's surface. Above them the huge cornice ripples in a continuous band, giving the appearance of keeping the whole building in a state of compression."
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After Michaelangelo's death, Carlo Maderno took over as architect and modified the design by adding a nave and façade. This changed the square exterior based on the shape of an equal sided Greek Cross (which had come to be associated with Paganism) to a rectangular exterior based on the Latin Cross (the new preferred symbol of Christianity).

Here is an aerial view of the layout based on Donato Bramante's original plan before it was modified by ideas from Raphael and Michaelangelo:
http://media-2.web.britannica.com/eb-media/25/5825-004-C3E4E1ED.gif

http://italian-architecture.info/ROME/16e.jpg

Aerial photo of the building:
http://www.greatbuildings.com/cgi-bin/gbg.cgi/St_Peters_of_Rome.html/41.902161/12.454156/18

Photographs of the interior, numerous diagrams of the layout, and plan drawings:
http://www.greatbuildings.com/buildings/St_Peters_of_Rome.html

Here is an extremely detailed description of the architecture and the history of designing the Basilica:
http://wapedia.mobi/en/St._Peter%27s_Basilica#3.