The Ender series contains three major arcs. These are, in publishing order:
 Ender series, the Shadow series, and The War of Gifts.

Normally, one would read in the publishing order, but you could read these arcs in any order.  Ender's Game, Ender's Shadow, and The War of Gifts are parallel novels that take place at the same point in time, from different perspectives. Their arcs then diverge from that point, from those unique perspectives. In fact, you could certainly read in a more-or-less chronological fashion:

 Ender's Game, The War of Gifts, Shadow series, Ender series.

The advantage of reading in a chronological order is that the direct sequels of Ender's game take place thousands of years in the future and are quite distant from Ender's game in terms of plot. When reading chronologically, the story evolves in a more fluid an direct way.

The books under each arc are as follows...

Shadow Series:
------------

 - Ender's Shadow Shadow of the Hegemon
 - Shadow Puppets Shadow of the Giant
 - Shadows in Flight (unreleased)

Ender Series:
------------

 - Ender's Game 
 - Ender in Exile (only
   chronologically, this is the most
   recently published book)
 - Speaker for
   the Dead
 - Xenocide 
 - Children of the
   Mind

War of Gifts:
-------------

 - A War of Gifts: An Ender Story