The Domestic Bliss Arc by Flamika
Pairing: Heero X Duo (1+2, 1X2)
Warnings: Yaoi, AR, continuing

Heero and Duo wind up living together after the series out of convenience. This is a series of shorts surrounding all the mundane aspects of their new lives in a completely non-mundane way. Wonderful!

Lolipop by ClarySage
Pairing: Heero X Duo (1x2)
Warnings: Yaoi, AU, complete, lemon

Everyday on his way to work, Duo sees [Heero] (I didn't know how to describe him) eating a red lolipop. UST ensues.

Love Letters by Clary Sage
Pairing: Heero X Duo
Warnings: Yaoi, complete

Heero gets a bit upset when Duo finds a love letter he wrote...addressed to him.

Sex With The Bartender by K
Pairing: Heero X Duo (1x2)
Warnings: Yaoi, AU, Lemon, Complete

Heero is a bartender who fights falling in love with a customer.

Falling Sideways by Blue Soaring
Pairing: Heero X Duo (1+2, 1X2)
Warnings: Yaoi, AU, complete

Heero and Duo have been best friends forever, but their friends and family seem convinced that they're dating, and the innuendoes and commentary are getting a bit annoying. The plan becomes to pretend to be hiding their relationship to get everyone off their backs, but...

Daydreams by D.C.Logan
Pairing: Heero X Duo (1+2, has a 1X2 sequel in the works)
Warnings: Yaoi, AU

Heero is an author with a horrible phobia of people and the world outside his appartment. It's so bad that he's almost never been outside since he moved in, though each morning he watches the braided man who runs the bookstore below through his window...

Love Trap by Amiko
Pairing: Heero X Duo, Zechs X Duo?!
Warnings: Yaoi, complete (has sequel)

Duo is sleeping with Zechs? Heero shouldn't care, shouldn't be so angry, shouldn't be... jealous?

Lust Pill by Amiko
Pairing: Heero X Duo (1+2, 1X2)
Warnings: Yaoi, complete, lime

Relena has sunk to a whole new level and is now relying on a lust pill to bring Heero's feelings to the surface. So why is heading back to his dorm?

Blue Bottled Belly Dancers by Clary Sage
Pairing: Heero X Duo, p-Heero X Duo (It's different!)
Warnings: AU, complete (has sequel), lemony

Duo is travelling in a foreign country and buys a bottle, but when an all-power djini pops out, his wishes become a little more than he was hoping for.  Excellent detail/characterization/writing. Just...
 

Being Duo Maxwell by Keelywolfe
Pairing: Heero X Duo
Warnings: Complete, yaoi

Duo's perspective of almost the entire series and his relations with Heero. Excellent characterization and just plain fascinating. Makes me want to re-watch the entire series.

Chained to You by Silverblade
Pairing: Duo X Heero
Warnings: Complete, yaoi

Duo does one thing in such a way that Heero's brain does the rest. Seriously, and it was pretty genius. Eventually though, Heero comes up with a solution to a problem that didn't actually exist. (Short, sweet.)

The Marble Duo by Lady Tora
Pairing: Heero X Duo
Warnings: AU, Fantasy, complete

Heero is a King and sculptor who, after much work over many months, completes a statue of Aphrodite for the goddess. When she asks what reward he wants, he asks for the one thing he can't have - love. There is no person in the kingdom worthy of King Heero, but eventually, Aphrodite finds a way to help him fulfill his own wish...

Skirt Pr0n Short by Ponderosa121 [Heero/Duo]
Gratuitous? Yes. Good? Hell yes. XD

Maintenance by D.C.Logan [Gen]
You have no idea how sad I am that DC Logan isn't writing anymore! She's definitely my favourite author for GW. This fic is part of a small series, but you can read it on it's own and enjoy it anyway. It covers the span of one day during which Duo is working on Deathscythe, is completely gen and just has a really good, solid but straightforward vibe going for it. The ending is what sold me.