There are several pilot-related short stories which have been published in the RPG magazines, first in the Star Wars Adventure Journal, and then in the Star Wars Gamer. When the Gamer ceased to exist after 10 issues, the SW Insider started to publish the short stories (the first one appeared in #62)
Various stories from the Adventure Journal were published in the books "Star Wars: Tales from the Empire" and "Star Wars: Tales from the New Republic". A few of them have a connection to Rogue Squadron (listed in light blue). As I've never read the Adventure Journal, I don't know if there are any other pilot-related stories that have never been published in a book; if so, please let me know.
Star Wars: Tales from the Empire
First Contact by Timothy Zahn
Tinian on Trial by Kathy Tyers
The Final Exit by Patricia A. Jackson
Missed Chance by Michael A. Stackpole
Hiding on Garqi after fleeing from Corellia and CorSec, Corran Horn becomes entangled with the Rebellion.
Retreat from Coruscant by Laurie Burns
A Certain Point of View by Charlene Newcomb
Blaze of Glory by Tony Russo
Slaying Dragons by Angela Phillips
Do No Harm by Erin Endom
Side Trip by Timothy Zahn and Michael A. Stackpole
Star Wars: Tales from the New Republic
Interlude at Darknell by Timothy Zahn and Michael A. Stackpole
The ways of Garm Bel Iblis and Hal Horn cross at Darknell.
Jade Solitaire by Timothy Zahn
Gathering Shadows by Kathy Burdette
Hutt and Seek by Chriss Cassidy and Tish Pahl
The Longest Fall by Patricia A. Jackson
Conflict of Interest by Laurie Burns
No Disintegrations, Please by Paul Danner
Day of the Sepulchral Night by Jean Rabe
Uhl Eharl Khoehng by Patricia A. Jackson
The Last Hand by Paul Danner
Simple Tricks by Chriss Cassidy and Tish Pahl
Beside the stories republished in the above mentioned books, I know only two Adventure Journal short stories, both by Timothy Zahn, and both dealing with Thrawn.
Mist Encounter by Timothy Zahn (published in Adventure Journal #7, I think)
Command Decision by Timothy Zahn
Star Wars Gamer
In Germany (I don't know about other countries, but I guess it is similar in most countries outside the US) the SW Gamer and the SW Insider are very hard to get. So if anyone of you doesn't have access to the issues listed below, but is interested in one of the short stories (or anything else), just drop me an email at firstname.lastname@example.org.
The Starfighter Trap by Steve Miller
Echo Flight defends Naboo against a threat from beyond and a traitor within (time period: Rise of the Empire).
Fair Prey by Daniel Wallace
Hunted by a mortal enemy with a twisted sense of fair play, Cecil Noone learns that life is anything but a game. (time period: Rebellion)
A Credit for Your Thoughts by Tish Pahl and Chriss Cassidy
Legendary smuggler Fenig Nabon cuts a deal with Talon Karrde and dodges blaster bolts on the desert world of Socorro. (time period: New Republic Era)
The Monster by Daniel Wallace
An ancient leviathan helps the Royal Security Force of Naboo uncover a sinister conspiracy. (time period: Rise of the Empire)
Bane of the Sith by Kevin J. Anderson
Fleeing the massacre at the Battle of Ruusan, sole survivor Darth Bane finds his destiny -- and confronts his demons -- on the beast moon of Dxun.
Deep Spoilers by Ryder Windham
Pride goeth before a long, long fall -- or, in the case of Spleed Nukkels and Neb Neb Goodrow, a deep, deep plunge.
The Crystal by Elaine Cunnigham
Jaina Solo takes her graduation present for its first -- and perhaps final -- flight. (time period: shortly before "Vector Prime")
Darkness Shared by Bill Slavicsek
The crazed Sith marauder Kaox Krul turns the tables on a Jedi Knight and her Padawan.
Rebel Bass by Kathy Tyers
Far Cry is just another backwater barn band trying to make it big on the dusk music scene. Or are they? Vye player Ry Ancum has a secret even his bandmates don't know.
Red Sky, Blue Flame by Elaine Cunningham
To the Chiss, heroism is for fools. (time period: around 20 ABY)
Battle on Bonadan by Greg Keyes
Uldir Lochet signed on to be a hero, but he had no idea the kind of trouble it would get him into. First episode of a new, six-part serial epic.
The Apprentice by Elaine Cunningham
How far will Jaina Solo go for revenge against the Yuuzhan Vong? A story set during the events of the "NJO: Dark Journey" novel.
Dark Tidings by Greg Keyes
Uldir Lochet and Jedi Klin-Fa Gi survived their last encounter with CorSec, but can they escape from Bonadan with the Yuuzhan Vong hunting them? Part II of our exclusive The New Jedi Order - Emmissary of the Void serial epic.
War on Wayland by Greg Keyes
The No Luck Requiered lies powerless, leaking air in the middle of nowhere. Will Uldir Lochet's crew survive? Part III of our exclusive The New Jedi Order - Emmissary of the Void serial epic.
Handoff by Timothy Zahn
Despite her training as an Emperor's Hand, even mara Jade is compelled to help a lost kid manipulated by forces beyond his control.
Star Wars Insider
Emissary of the Void: Episode IV Relic of Ruin by Greg Keyes
Insider's premier installment of Greg Keyes' the New Jedi Order serial drops you right in the middle of the action. Catch up on the first three installments for free at starwars.com.
Emissary of the Void: Episode V A Perilious Plan by Greg Keyes
Rescue pilot Uldir Lochet, rogue Jedi Klin-Fa Gi, and the crew of No Luck Required risk everything to escape Yuuzhan Vong forces over Wayland.
Emissary of the Void: Episode VI by Greg Keyes
Can Uldir Lochet stop the Yuuzhan Vong plan to cripple the New republic, or will he unwittingly help them? The exciting conclusion the the New Jedi Order serial adventure.
The Pengalan Tradeoff by Aaron Allston
Joram Kithe is a Republic accountant who's dodged responsibility his entire life. Somehow he's ended up stranded on the battlefield in charge of a clone trooper platoon. (time period: during the Clone Wars)
Elusion Illusion by Michael A. Stackpole
Jedi Knight Aayla Secura wonders why Master Mace Windu chose her for such a crucial mission, but soon she learns she might be all that stands between Corellia and the Separatists. (time period: during the Clone Wars, just after the Battle of Geonosis)
The Trouble With Squibs by Troy Denning
After the events of 'Tatooine Ghost,' Han and Leia do a little art shopping, Solo style. (time period: ca. 8.5/9 ABY)
Hero of Cartao: Episode I Hero's Call by Timothy Zahn
The world of Cartao, home of Spaarti Creations, sits near the front lines of the galaxy-wide Clone Wars. Neither the Republic nor the Separatists have shown an interest in it - until now. (time period: during the Clone Wars)