The West Wing
Josh/Donna all the way, with a smattering of gen and other ships.
The National Library
Took over where the West Wing Fanfic Archive left off, and is doing a pretty nice job. The automated indexes are excellent, everything is rated, and everything is formatted to be readable. Every pairing is represented, and the archive itself is gorgeous. Well worth a visit if you have some time to kill.
The Bondi Gargoyle
The Gargoyle offers up for amazing (if sometimes punctuationally challenged) Josh/Donna stories -- Snowbowl became an instant classic, as Josh accompanies Donna home to pose as her fiance, and gets a lot more than he bargained for; the As You Wish series is just a cool romance; Big Shoes puts Josh into Leo's job, with all of the complications that entails. You will always walk away from the Gargoyle's stories happy and satisfied.
The Syntax of Things Unspoken by Ygrawn
"Adjective, Verb, Noun, Adverb. Past imperfect. Future tense. Present reflection. Four stories with no split infinitives." Beautifully written and executed West Wing fic -- the language is gorgeous, the characterization perfect, and there's humor and angst balanced nicely. Go read it, then try the rest of Ygrawn's work -- it's largely very well done (and quite maturely executed) Josh/Donna, and it's almost uniformly excellent.
The West Wing Fan Fiction Archive
No longer updated, but still a large, reasonably well-organized resource. Most of the stories are labelled by category/couple, but 'shipper fics can sneak under the radar; if you violently hate a pairing, be on your guard. Quality varies widely, but the majority is at least readable. Read Adrienne, who sets the standard for Toby fic; Andrea (The Pursuit of Happiness); Jennifer Fry for good CJ/Toby; Lida Rose for fun and fluffy CJ/Danny; Sheshat, whose Soap Operas and Soap Suds is a gem; and Sheila Moriarity, another CJ/Toby writer.
SheilaVR simply rocks. Refiners Fire is one of the best of the post-season 1 finale fics, Shadow of a Gun is a strong Margaret-centric story, and And the World Stood Still is a compelling drama.
Jenny's Old School West Wing Archive
Reasonably well-organized, if no longer updated, it features many of the same authors as The West Wing Fanfiction Archive, but also has several authors not archived there. Lots of 'shipper fic, but it's separated out by category.
Crash Into Me is almost universally acknowledged as one of the strongest and most absorbing Josh/Donna series ever written. Beginning with an unspeakable tragedy, Pix takes the pair through a relationship in which nothing is ever, ever easy, everyone has to learn to stand alone, and finding out where home is, is the hardest thing they'll ever do. Begin with the prequel Just Friends, or dive directly into Best Served Cold.
Allison is the queen of sweetness and light, and I mean that in the best possible way. If you want to be happy, to get a great WAFF and to giggle endlessly at the cuteness that is J/D and S/A, she's your woman. Start with the "Lessons" series (Downtime, The Company of Women and Lessons) or the Great Expectations series, and don't miss Vision for a sweet post-shooting vignette between two characters you wouldn't expect.
Jennifer's fics range from the sweet to the schmaltzy. I loved In a Cold Season, and Back to School was chock full of WAFFs.
The West Wing Fantasy 8
18 'episodes' of a somewhat Josh/Donna-centric virtual season, but if you're not onboard the Good Ship J/D, don't let that throw you -- this is a well-plotted collaborative work that could very well have done the job on-screen. Politics and relationships are juggled handily in multiple plot lines, the characterization is divine and yeah, Josh and Donna finally get some happy-ever-after (which doesn't come easily, but you had to expect that). Very highly recommended for anyone who loved The West Wing.
An archive showcasing novel-length 'West Wing' fics. Try SheliaVR's All Things Being Equal to start -- someone's been reading way too much Clancy, and it shows. But the novel is extremely well done, full of adventure and angst, as a state visit to a nuclear sub goes terribly wrong, and the consquences could be world-changing. Solid characterization, a ton of research and SheilaVR's usual gift for words make this a story that shouldn't be missed.
The Joshua Monologues and Other Tales
Depressed about seasons 4 and 5 of West Wing? SpitztheCat serves up some funny, WAFFy, true-to-character romance, smut and life. NC-17, and proud of it. She also has some solid stand-alones disinguished by her near-inability to write them without massive levels of angst. < g >
Fanfic With Footnotes
Jo March and Ryo Sen are one of my favorite writing teams in the universe. Their Josh/Donna stories, beginning with An Innocent Kiss and continuing through the A Winning Strategy series are absolutely exceptional -- sharp dialogue, tight plotting, realistic to the point of trauma, and (mostly) dead-on characterization. Then there's the Partyverse.... Go. Read. Now. Even if you're not into Josh/Donna. Trust me on this. If you want good CJ, you can't go wrong with any of Ryo's stand-alones, particularly Drunk and Quartered; to find out how everyone wound up oputside Donna's window on Inauguration night, try her Solecism, co-written with Marguerite.
The Collected Ramblings of Puck and Zillah
Another fabulous collaboration. Together or separately, Puck and Zillah write strong, realistic romances for Josh/Donna and Sam/Ainsley, combining solid characterization and wicked humor with some fabulous smut. Start with Namesakes and just keep going, or dive in with White House or Bust.[No idea where they went, but I'm keeping the link listed on the off chance that they'll return.]
Transfigured Night With a Strange Communion is one of the best of the post-18th and Potomac stories, and the Time and the Fates of Man trilogy are solid, absolutely unique looks at 'In the Shadow of Two Gunmen'. Descanso is one of the few fics to deal well with the aftermath of Zoey's kidnapping, and for possibly the best post-administration fics ever, read all six parts of The Rarest Faith. She also does "The X-Files" fic that I assume is just as solid.
Sally's West Wing Fanfiction
Yay, Sally discovered J/D! It's all good, but the standout is Unspoken, a painful, serious, thoughtful, excellent Josh/Donna novella -- it's the Santos administration and Josh and Donna do a lot of talking, but not much listening, until everything implodes. Absorbing, but way angsty.
State of the Union
Fic by Jori and MoJo, yet another great writing team. Their Josh/Donna series starting with Opportunities rocks (NC-17, but with R versions available), and their other stuff ain't bad, either. Pretty graphics, too. (I think Jori produced the first piece of Sam/Ainsley smut; how's that for a mark on the world?)
Wednesday Night Rants
Home of someone who does Aaron Sorkin as well as Aaron Sorkin does (often better). Her series of episode continuations (and a few stand-alones now) is absolutely fantastic and not to be missed. Then cruise over to Tuesday Night Rants for her equally excellent 'Sports Night' fic.
Dee's Josh & Donna Fanfic
I love this woman for her ability to build several completely separate romances, in a variety of alternate universes, for the same two people, and keep them all different. The Something Stupid series is perfectly in character, her smut is emotional and hot, and Bedford Falls is one of the best AU's I've read in any fandom.
Bramble's Josh and Donna Fanfic
Bramble gives good romance, handles every character she addresses well, and writes good smut (she'll try anything once)! Exhibit A is screamingly funny, Problems is just cool bonding-type stuff, Giant Waffles and Tree Sloths rocks, and 20 Hours in Wisconsin... let's just say you'll never look at ice cream the same way again.
Navigating by the Stars
I wish CazQ would write more West Wing; the two stories she's produced are two of my favorites. Only in the Cold is a beautiful, poetic trip through Sam Seaborn's mind, slipping through a campaign and two years in the White House, and all the ways friendship and politics can make a good man wonder and worry and hurt. Bittersweet and painful and gorgeous. For something completely different, Burning Houses, Burning Bridges, a J/D piece from Josh's POV (always a neat trick) that reads realistically and romantically and perfectly in character all around.
There's very little on the WingNuts page that doesn't rock, but The Quest is particularly impressive. Sam and Leo are worried about Josh and Donna's subtext, a couple of friends of Josh's are gleefully encouraging the subtext, Josh and Donna remain more-or-less oblivious to the subtext, and everyone else is much more interested in winning reelection than in anyone's subtext. They finally finished, and promptly dove into a sequel, so it's not over yet! While you're waiting for the rest of Heaven and Hell, go read Off to Camp, but if you do it in public, the giggling is going to get you some really funny looks.
The Age of Aquarius by Speranza
This makes me remember the days when it was all about the Josh/Donna -- in the good way. Beautiful Josh voice, explaining exactly why he doesn't want to get involved with Donna, and it's actually a really good reason. Which, of course, doesn't stop him from finally just going for it -- in his own insane and gleeful Josh-ian way. If this had played out on screen, I would have been so totally happy, I can't tell you. Just reading it gives me a warm, happy glow. Also read The Politics of Love: miscommunication and wires crossed and really, how would Josh and Donna be any different if they were married? Short and awesome and, oddly enough, from Sam's POV. It works.
Boulevard of Misdirection
Jaye is another writer of unashamed fluff, and I can respect that. Her Friendly Skies, for instance, is one of those stories that just makes you all giggly and WAFFy as you read. The J/D shippiness is mostly in the subtext of well-written fluff involving a kite, a picnic, and two friends hanging out and being happy being co-dependent. Try it, then browse through the rest of her archive.
In This World by little zigzags
"There's nothing but a voice-like left inside\That seems to tell me how I ought to feel,\And would feel if I wasn't all gone wrong." J/D. (Also try Necessary.)
The People's Servants by Speranza
Big Block of Cheese Day, Santos Administration. Short and perfect.
Prudence by coffeeplease
"Well, now she had beaten C.J. at something. She was the first pregnant press secretary." Really kind of adorable J/D, in a slightly AU Santos administration.
They Can't Take That Away From Me by Mahc and WWNeurosturgeon
The authors hit Inauguration in West Wing continuity, then immediately take a hard right, spping out an alternate way that night could have gone. When the President collapses in the middle of a city-stopping blizzard, Abby is the only doctor available to try to save her husband, while Leo and CJ try to cope with Jed's illness, Qumari aggression and a over-eager reporter who draws the wrong conclusions at the wrong time. A strong, insightful character study of families and governments; the dialogue isn't quite as sparkling at Sorkins, but the characterization is stronger, and never falters.
Lots of good stuff, although there's little fic being written for the ship anymore, and did I mention I run it? Allison is at it again with the Haven series; also try Scott Fendermaster's Retaliation for great friendship fic for S/A and a solidly plotted story for everyone else. And do not miss Much Ado About Politixs from Mich -- it's barely S/A, but I made an exception since it's such ill, sick, twisted genius.