In general, the books assume that you've read everything previously released. The nomenclature also evolved throughout the series, and going out of publication order will lessen one's reading experience. This doesn't matter as much regarding the short stories, but should be followed regarding the main books.
Here's an up-to-date infographic I put together showing the relationship of the different books in the series. In general, books should be read in publication order, though it matters less if they're not directly connected story-wise. The unconnected short stories can be read whenever:
It should be stressed that pretty much every book in the series has a wildly different tone and style. Liking (or disliking) one book doesn't mean you'll like or dislike a different one. If you find you don't like what you're reading just put it down and jump to the next number on this list (only the ones grouped under a single number are strictly linearly dependent and similar in tone):
- Ender's Game
- Speaker for the Dead trilogy1
- Speaker for the Dead
- Children of the Mind
- Investment Counselor (short story)
- Ender's Shadow1
- Shadow trilogy
- Shadow of the Hegemon
- Shadow Puppets
- Shadow of the Giant
- Ender in Exile
- Shadows in Flight (novella)
- First Formic War trilogy1
- Earth Unaware
- Earth Afire
- Earth Awakens
- Second Formic War trilogy
- Fleet School
- Children of the Fleet
- Renegat (novella)
- Messenger / Shadows Alive (announced)
1can be really be read right after Ender's Game.
Other short stories and novella
(Other then the two listed in the previous section) these are mainly optional side-stories and can be read anywhere after Ender's Game.:
- The Polish Boy
- Teacher's Pest (after The Polish Boy)
- Mazer in Prison
- Pretty Boy
- The Gold Bug
- Governor Wiggin (after The Gold Bug)
- War of the Gifts
- Ender's Stocking
- the upcoming novella from Cetipede Press
Orson Scott Card's official answer (as of 2009, so not covering Formic Wars and Fleet School) is to pretty similar to this. He recommends publication order for the novels, but advises younger readers to push off reading the Speaker trilogy. He says to hold off on the short stories until after Ender's Game.
Full quote follows (in spoiler text cause this answer is already long and some devices truncate unopened spoiler text blocks.)
The "preferred order" depends on what you mean by "preferred," and who's doing the preferring.
There are two main story threads. One begins with Ender's Game, and proceeds to Ender in Exile (which overlaps with EG) and then on to Speaker for the Dead, Xenocide, and Children of the Mind.
The other story thread begins with Ender's Shadow (which is parallel to Ender's Game), and proceeds to Shadow of the Hegemon, Shadow Puppets, and Shadow of the Giant. Eventually the two threads come together with the book Shadows in Flight.
The short stories make things even more complicated. They should NOT be read in chronological order because even though many are prequels, they only take on their full significance if you have already read either EG or ES.
The Polish Boy and Theresa (in First Meetings) are the stories of Ender's parents - who they are and how they meet. Mazer in Prison (IGMS) is the story of Mazer Rackham's recruitment by Graff to be part of the training of the future commander of the fleeet.
The stories Cheater and Pretty Boy are the stories of Han Tzu (Hot Soup) and Bonzo Madrid when they were children on Earth, before going to Battle School.
Goldbug (standalone comic and IGMS story) takes place on the first world Ender goes to, where he discovers the hive queen. It slides into the middle of Ender in Exile ... somewhere ...
Investment Counselor (First Meetings) takes place after EG and Ender in Exile, and before Speaker for the Dead.
The story War of Gifts (a novella) takes place in the midst of Ender's Game - sort of a side story. It can stand alone. There is also an IGMS story called Ender's Stocking that overlaps with War of Gifts but focuses on a crucial time in Peter's life.
The stories A Young Man With Prospects and Ender in Flight are both part of Ender in Exile, so if you've read that novel, you've read those stories.
You can read the novels in the order of composition: Ender's Game, Speaker for the Dead, Xenocide, Children of the Mind, Ender's Shadow, Shadow of the Hegemon, Shadow Puppets, Shadow of the Giant, and Ender in Exile. (This poses the challenge for younger readers of the very talky, philosophical and adult Speaker, Xenocide, and Children of the Mind.)
You can read the novels as two separate threads in sequence. For younger readers, the best plan is to read Ender's Game and Ender's Shadow in any order, and then proceed through the Shadow books and then all the shorter works, saving Speaker, Xenocide, and Children of the Mind until you're older.
Or you can struggle to read them in chronological order of the story, as described above.
Then again, the Empire books, the Homecoming series, and the Alvin Maker books are absolutely in chronological order and are very clear. They have nothing to do with Ender Wiggin or Julian "Bean" Delphiki, but at least you know what order they're in!
I know, the question seemed to be focused on the written works, but I thought I may as well cover the comics too. The comics were made after the books were already written, and so the publication order doesn't really matter. For the Comics, I would go with a modified chronological order starting with Ender's Game. Note that Ender's Shadow arc isn't necessary for understanding any of the other comics.
- Ender's Game: Battle School
- Recruiting Valentine2
- Ender's Game: Command School
- Ender's Shadow: Battle School
- Ender's Shadow: Command School
- War of Gifts2
- The League War2
- Mazer in Prison2
- Ender in Exile
- Gold Bug2
- Speaker for the Dead
- Formic Wars: Burning Earth
- Formic Wars: Silent Strike
2These are one-shots and can easily be skipped.