Almost solely Tony/Pepper-centric, with some straight drama or humor thrown in for variety.
Almost No One Makes It Out by atrata
What if Tony Stark had the brains and the attitude, but not the money and fame? A really well-done military AU, carefully thought out and awesomely plausible. Recced by practically everyone.
Books and Backchat by A Wandering Bard
A gleefully random manifestation of spectacularly perfect Tony and Pepper dialogue.
Engine of Survival by marinarusalka
Yinsen's story, and it's perfect.
A Small and 100% Innocent Token of Gratitude by Kate Andrews (svilleficrecs)
Oh my god. Incredibly hot, fabulously in-character, absolutely believable Tony/Pepper. And did I mention the hot? Oh my god. NC-17
It Takes a Village to Raise a Tony Stark by hackthis
To quote musesfool, "Tony Stark in all his charming yet dysfunctional glory, with Jarvis, Rhodey, Happy, and Pepper along for the ride."
"The Kids Aren't All Right" by Christine Everhart (vanityfair.com) by samdonne
The article Christine Everhart writes a year after "the" press conference. One of those works that makes me slightly depressed because I will never write anything this amazingly good, ever.
Drink Deep by dafnap
Extremely hot Tony/Pepper vignette. Yowsa. PG-13
Five Rumors About Tony Stark That Aren't (Entirely) True by hackthis
Go with it, okay? Totally worth the price of admission, particularly the last two bits. For something slightly more serious, try Employer/Employee Relations -- intelligent, rational Pepper voice on How to Fall in Love With Your Superhero Boss and Live with It. (Tony/Pepper).
Four Times Pepper Considered Quitting and the One Time She Did by seren_ccd
A nice little character study of Pepper and why she does what she does.
Grease-stained by nekare
"Ever since Afghanistan he's been working on reshaping his moral code, adapting it to the man he is now instead of the boy he was when his parents died. It's both terrifying and liberating." Tony/Pepper-ish
Hot Rods and Kleenex by bacchae23
Sweet and awesome Tony/Pepper vignette.
Miscellaneous Is Always the Largest Category by Splash the Cat
Pepper's job encompasses many things, some of them more annoying than others...
Prompt Responses by mekosuchinae
A series of short responses to varyingly Tony/Pepper challenges with a remarkable touch for the characters.
Proof by gabrielle
Fluffy Tony/Pepper, with nice banter and an adorable robot. Her Posthuman also rocks.
Reconciliation by thelma_lou
Tony and Pepper in a relationship, handled with an adult awareness of reality and an understanding of both characters. One of my favorites for this ship. Relinked to a different journal so everyone can read it.
That Time With the Dobermans (and the Hole in the Wall) by mspotts
Pepper gets kidnapped and Tony saves her (sort of).
This Is How It Works by hitlikehammers
Tony/Pepper from his POV, for once. Somewhat angsty, but convincing.
Tony and Pepper Go to Target by aj
Silly, remarkably in character, and awesomely fun. You may snort coffee out your nose at at least one point.
Two Kinds of Ice Cream by VR Trakowski
Happy/Natasha. No, seriously. And it works! Very nicely characterized, fleshing out two secondary characters, and quite adorable. KikiRec
Well Heeled by amonitrate
A nice little snapshot of mundane things that adds up to a lovely look at Pepper's relationship with Tony.