I only know of one that fits the bill - its a future fic set a few yeas after Trinity where Rodney is raising Madison #9The title of the series is Raising Madison#0 you may have already read it but its the only future-fic McShep domestic I can think of. The others were straight out AU's.
Here is the link; http://www.hawksong.com/~thammill/SGA_Fic/SGA.htm (scroll down to find the link to the first story Bell's Theorum~).
maybe try these? War Bride (http://trickster.org/speranza/cesper/Warbride.html) by speranza Scenes From a Practically-Marriage (http://zinfic.livejournal.com/84802.html) by zinnith Tea and Sympathy (http://sabinelagrande.livejournal.com/201532.html) by sabinelagrande (John + Ronon friendship, about John/Rodney domesticity) The Tragic, Doomed, and Epic Life and Loves of Elizabeth Jean McKay, Plus Other Interesting Stuff (http://captanddeastar.livejournal.com/2187.html) by deastar there's also casa_mcshep...
It's All Your Fault Radek, You Meddling Bastard (http://gateslashers.webs.com/iayfrymb.htm) by fawkesielady_ed is an AU were the boys end up in domestic bliss, though it's about them getting there and has nothing to do with Atlantis. Veterinarian!Rodney (teehee). It's a very fun story. Donno if it's quite what you're looking for, but it's the first thing I thought of.
no subject
Date: 2010-02-25 01:26 am (UTC)Here is the link; http://www.hawksong.com/~thammill/SGA_Fic/SGA.htm (scroll down to find the link to the first story Bell's Theorum~).
no subject
Date: 2010-02-25 02:13 am (UTC)War Bride (http://trickster.org/speranza/cesper/Warbride.html) by speranza
Scenes From a Practically-Marriage (http://zinfic.livejournal.com/84802.html) by zinnith
Tea and Sympathy (http://sabinelagrande.livejournal.com/201532.html) by
The Tragic, Doomed, and Epic Life and Loves of Elizabeth Jean McKay, Plus Other Interesting Stuff (http://captanddeastar.livejournal.com/2187.html) by deastar
there's also
no subject
Date: 2010-02-25 05:14 am (UTC)no subject
Date: 2010-02-25 12:32 pm (UTC)no subject
Date: 2012-03-18 04:10 am (UTC)Bonus: It was long! I LOVE long mcshep stories <3