For my own reference
John/Dean/Sam fics
In some of them the trio is faintly there, in others it's clearly obvious.
In some of them it's either John/Dean with Sam slightly off to the side or Sam/Dean with John slightly off to the side, but I tried to keep to the ones where there was sexual tension between all three players.

Shea's (sheaseth) As Silver Refined
a prequel and 10 parts
http://www.journalfen.net/users/sheaseth/tag/as+silver+refined


A Daisy If You Do
by Mortified1
http://www.livejournal.com/tools/memories.bml?user=mortified1&keyword=Daisy&filter=all
it has 11 parts to it

Surrender Sam/Dean with John
by Drvsilla
http://drvsilla.livejournal.com/38890.html
sequel Capitulation
http://drvsilla.livejournal.com/100656.html


Troika (30 parts)
by noword4it
http://www.livejournal.com/tools/memories.bml?user=noword4it&keyword=troika&filter=all

Trinity
by noword4it
http://noword4it.livejournal.com/1599.html


The More You Shake, The More You Give Away
by bloodymaryspn
http://bloodymaryspn.livejournal.com/1289.html
sequel When you hide, hide inside that body
(John/Dean, Sam/Dean, Bobby/Dean, implied Bobby/John)
http://bloodymaryspn.livejournal.com/2126.html


Bloodlines
by Rei_C
http://www.library.the-arcades.com/bloodlines1.html
also by Rei_C
Golden in the Mercy of His Means (purr-verse)
http://library.the-arcades.com/goldenmercy.html


By theyscreamofyou
degausser
http://theyscreamofyou.livejournal.com/10700.html
sequel Milstone
http://theyscreamofyou.livejournal.com/11090.html
also by theyscreamofyou
Nice and blue
http://theyscreamofyou.livejournal.com/10378.html
walk the rain
http://theyscreamofyou.livejournal.com/19074.html


El Camino Real (The King’s Highway)
by Hope (angstslashhope)
http://hope.oscillating.net/2006/09/28/fic-el-camino-real-the-kings-highway/
sequel And the little one said
http://hope.oscillating.net/2006/10/12/fic-and-the-little-one-said/
sequel And then there were two (just John/Dean)
http://hope.oscillating.net/2006/11/30/fic-and-then-there-were-two/

also by Hope
Perhaps, Perhaps, Perhaps
http://hope.oscillating.net/2007/01/01/fic-perhaps-perhaps-perhaps/


Unkept Secrets
by Melly Sue (Jellybean_Slash)
http://jellybean-slash.livejournal.com/148051.html


Succupire ~ Kindaric Scrolls Prophecy
aetheruk
http://aetheruk.livejournal.com/21749.html


By bloodkisses/SangEmbrasse:
Laying claim
http://sangembrasse.livejournal.com/22950.html
Claim Relinquished
http://sangembrasse.livejournal.com/23330.html


By Xantissa
The Sins and Desires series of fics
(which are soon to be friend's locked according to the author)
Taking Orders http://xantissa.livejournal.com/5212.html J/S/D
Keeping Secrets http://xantissa.livejournal.com/8806.html J/S/D
sequels:
http://xantissa.livejournal.com/7783.html (sam/bobby)
http://xantissa.livejournal.com/13021.html (john/dean)
http://xantissa.livejournal.com/13021.html (dean/sam)


Time out
by vileseagulls
http://vileseagulls.livejournal.com/342034.html


Wolf
by Hellskitten (crissyd33)
http://deannaz.livejournal.com/75672.html
http://deannaz.livejournal.com/75812.html
http://deannaz.livejournal.com/77971.html
http://deannaz.livejournal.com/78247.html
http://deannaz.livejournal.com/78445.html
http://deannaz.livejournal.com/78777.html
http://deannaz.livejournal.com/79076.html
prequel Pretty (gen)
http://deannaz.livejournal.com/84440.html
sequel Sleeper (John/Dean)
http://deannaz.livejournal.com/84512.html
http://deannaz.livejournal.com/84850.html


Splintered
by Phantisma
http://phantisma.livejournal.com/tag/splintered
http://phantisma.livejournal.com/108711.html
http://phantisma.livejournal.com/108854.html
http://phantisma.livejournal.com/109099.html
http://phantisma.livejournal.com/109451.html
http://phantisma.livejournal.com/109689.html
sequel Shattered by Phantisma
http://phantisma.livejournal.com/151657.html
http://phantisma.livejournal.com/152023.html
http://phantisma.livejournal.com/152079.html
sequel Scattered
http://phantisma.livejournal.com/155818.html
http://phantisma.livejournal.com/156120.html
http://phantisma.livejournal.com/156301.html

by Phantisma
Almost
http://phantisma.livejournal.com/94150.html
In sweat and blood
http://phantisma.livejournal.com/146527.html
http://phantisma.livejournal.com/146819.html
http://phantisma.livejournal.com/147118.html


Woodsmoke and Crisp Red Apples (unfinished wip)
saekokato
http://community.livejournal.com/snslashnotebook/102583.html
http://community.livejournal.com/supernaturalfic/596713.html


Two wrongs don't make a right
and
Three is the perfect number
by the Perv Collective
http://www.disanddatbycj.com/collective/Collective01.htm


Dirty Bad Wrong
by Aracle
http://aracalefic.livejournal.com/1541.html


Spanish Fly
by Robin Serrano
http://robin-serrano.livejournal.com/12622.html


Shaky ground (s/d hinting at j/d)
by Damerel
http://damerel.livejournal.com/30985.html


The JW Hustle
by Miss Meehan
http://www.fanfiction.net/s/3072040/1/The_JW_Hustle


Sit A Spell
by Nyghtpet
(the first drabble in the entry)
http://nyghtpet.livejournal.com/161186.html


Laundry Day (more Dean/Sam & Dean/John than a real 3some)
by missmalachite
http://community.livejournal.com/wincest/506371.html


Father Figure (John watching Sam/Dean)
by Mango_butter
http://mango-butter.livejournal.com/1778.html
http://mango-butter.livejournal.com/3023.html
http://mango-butter.livejournal.com/3315.html


All That Stands Between Us (more John/Dean)
by Ellipsis Black
http://community.livejournal.com/sn_slash/423212.html
sequels Father's keeper (more Sam/Dean)
http://community.livejournal.com/sn_slash/444224.html
and The Winchester code (Sam/Dean)
http://community.livejournal.com/sn_slash/446857.html


Sammy Already Knew
by Dontmembersam
http://dontmembersam.livejournal.com/9511.html
http://dontmembersam.livejournal.com/10023.html
http://dontmembersam.livejournal.com/13076.html


Daddy Drinks Because You Cry
by Marishna
http://marishna.livejournal.com/405740.html


Everything’s Faster when Standing Still
by Andrea (silent flux)
http://silentflux.livejournal.com/74616.html
(Winchesters aren't related)


All About Feeling Good
by Eboniorchid
http://writingbyebonio.livejournal.com/33311.html


Eros
by Auryn
http://auryn-wren.livejournal.com/3483.html


By The Light Of The Moon (more toward John/Dean, Sam/Dean)
by Ianthe Aveira
http://ianthe-aveira.livejournal.com/8080.html
http://ianthe-aveira.livejournal.com/8862.html
http://ianthe-aveira.livejournal.com/12994.html
http://ianthe-aveira.livejournal.com/20047.html


Unveiling Series
by Shorts
http://shorts7.livejournal.com/95475.html
http://shorts7.livejournal.com/121708.html
http://shorts7.livejournal.com/134605.html
http://shorts7.livejournal.com/157430.html


Can’t Say No
by Flinchflower (almost a gen fic)
http://community.livejournal.com/wincest/645934.html


The Devil You Know
by Lilmissfury (Liz) demonJohn
http://lilmissfury.livejournal.com/61486.html


Fine Young Knives
by Blue Soaring
http://blue-soaring.insanejournal.com/10817.html
also...
this has daddyCest overtones:
Time Wastes Itself
http://blue-soaring.insanejournal.com/10180.html


Dean’s Dirty Desire
by Demona aka azraelz_angel
http://community.livejournal.com/rounds_of_kink/150651.html


Redeeming Value
madame_meretrix
http://madame-meretrix.livejournal.com/16167.html


Our Driving Force
honeyone
http://honeyone.livejournal.com/119072.html
John watches


The Most Exquisite Sin
honeyone
http://honeyone.livejournal.com/119446.html


Title: Lessons
Author: ianthe_aveira
Pairings/Characters: John/Dean, Caleb/Dean, Sam/Dean
http://ianthe-aveira.livejournal.com/53788.html