Non-Jerk John:

Don't Ask, Don't Tell (http://dodger-winslow.livejournal.com/52387.html) - if you like this, try more of her stories. She writes John pretty well in my opinion.
"If we got in a wreck, and Sammy and I were both unconscious, and the Impala caught on fire so you only had time to save one of us, who would you save?"

Live Again (http://foxlives.livejournal.com/4182.html) - this has some mild/implied Sam/Dean
John Winchester's Favorite Christmas

Golem (http://sandymg.livejournal.com/16088.html)
Dad's in Minnesota keeping secrets, Dean's picked up a solo hunt, and Sam ... where is Sam?

I've read Don't Ask, Don't Tell, but I'll read it again for the sake of it.

I'll definitely look at the pther two

I mean, other two.

Close Ecounters
http://archiveofourown.org/works/46791?view_adult=true
summary: It's the same old story: boy meets space alien, boy sleeps with space alien, boy's brother is mortified.

I love this fic, its hilarious :)
Its Dean/cas :)

I will definitely check this out

John's probably my favorite SPN character after Sam and Dean. Here are a few of my favorite pre-series stories:

One Too Many (http://ficwriter1966.livejournal.com/241022.html#cutid1) by ficwriter1966
On his way to Pastor Jim's in Minnesota for Christmas, John Winchester and his two little boys find refuge from a blizzard at a dinner with nine other travelers. Wonderfully creepy story with bad-ass papa John.

Shotgun (http://july-july-july.livejournal.com/37611.html#cutid1) by july_july_july
Instead of moving constantly, John Winchester settles down in Dillon, Texas, with his boys. Gen, Pre-series, AU, crossover between Supernatural and Friday Night Lights.

Harvester of Eyes (http://community.livejournal.com/spn_boc/6283.html) by gwendolyngrace
Summary: Supernatural / Sandman crossover. John gets wind of a hunt that he doesn’t want the boys anywhere near. But taking them far from danger actually puts them in its path, when they stumble into an open doorway to the Dreaming.

A Loaded God Complex (http://community.livejournal.com/spn_summergen/36099.html) by gwendolyngrace
Summary: The demon-worshipping cult that John has been tracking chooses Sam’s Middle School as their target. But John doesn’t know that there’s already another investigator on the case. Medium crossover (but pre-series, so not necessary to know anything about Medium).

Coming Down on a Sunny Day (http://maychorian.livejournal.com/233162.html) by maychorian
Summary: In 2009, Castiel watches the Apocalypse end disastrously and makes a decision. In 1984, John Winchester suddenly finds himself with another little boy on his hands, one with dark, messy hair and sad blue eyes who won't leave John and his sons alone. And so Sam and Dean get a weirdo big brother. Because their lives aren't complicated enough.

little rattle stilt (http://archiveofourown.org/works/475) by Hope
Summary: Circa 1988-9. Sam gets taken by the CPS.

The Littlest Hunter (http://users.livejournal.com/_bluebells/32367.html) by bluebells
Summary: As punishment for disobeying, Castiel is sent back in time in the form of a young child - only to be unofficially adopted by John Winchester.

The Usual Bad News (http://loki-scribe.livejournal.com/24289.html#cutid1) by loki_scribe
Summary: John showed up at Bobby's with a Wild Hunt on his tail. What was he expecting if it wasn't homemade explosives and someone to watch his back?

The Hapless Soldier's Sigh (http://bad-peppermint.livejournal.com/10583.html) by bad_peppermint
Summary: In the summer of '88, a man called Frederic Lance summons John Winchester to Montana to find out who or what is killing off a small town's children. Burdened with a demanding five-year-old, a reclusive nine-year-old, and an employer who doesn’t hide his issues with John’s parenting methods, John could do without a case that has no leads, no M.O., and no clues except for a whole lot of field mice and some body parts. And what kind of monster is this interested in teeth?

Past is Prologue (http://www.fanfiction.net/s/4017853/1/Past_is_Prologue) by camlann
Sometimes, the past can be both a blessing and a curse. For John Winchester, a walk down memory lane could prove to be more than he bargained for when he's suddenly faced with the unexpected, in the form of two eight-year-olds. (WIP)

And anything by dodger_winslow (http://dodger-winslow.livejournal.com/108187.html).

Thank you for so many recs. I've read a couple of these, but for the most part I haven't heard of them. Thank you, again.

The one I can think of for your werewolf request is Mummyluvr's werewolf series. I like Mummyluvr. She was young when the story was published, and her style shows that, but she's got an excellent grasp of plot and knows how to whip up solid entertainment.
Sam and Dean are running from John. But do they have to?
http://www.fanfiction.net/s/3748389/1/The_Change
http://www.fanfiction.net/s/3765395/1/Flux

This one has Sam as the wolf, but you might like the way it revolves a lot around John. It's WIP, advancing slowly, but it's very good.
Mikya2200's Unleashed Verse
http://mikiya2200.livejournal.com/11407.html
Mikya 2200 has a lot of other good John fics.

Mooney-Magnolia, like Mummyluvr, has a youthful style, but also a great work ethic, involved plotting, and an overriding sense of fun. If you like creature fics, she has several, all long.
In Red Hot Moon, Sam has always been a werewolf, but eventually Dean gets bit, too. John is not the ideal parent, but he's not an asshole.
http://www.fanfiction.net/s/5303036/1/Red_Hot_Moon

Thanks for the recs. I've read Change, but I don't think I've read Flux, so thanks.
Going to go read these now.

Mate and Pack
"Dean gets bit by a werewolf. Sam and Cas have to show the wolf that they are pack and not a threat, but something unexpected happens
(R?)

take you as you are
"http://community.livejournal.com/spn_hardcore/257634.html
(R?)

(i think these were racy but i cant remember)

"3 Kids and a Shitty Dad series (although i dont think he come out that bad. Has wee!Cas also)
"http://zimothy.livejournal.com/617.html

and this awesome somewhat AU series where the Winchesters move next to the Novaks (kids Michael, Gabriel, Anna, Cas) after Mary dies in fire
(author master link post so you can get to both)
http://wildsky.wordpress.com/supernatural/

The Sound of Silence by wildsky_sheri (also on on deancastiel)
John’s POV. John’s not really sure what to make of the weird kid who seems to have mind-melded with his son.

if i was a cloud in the sky
John’s POV. “We wish to attend snufflegarten,” Castiel announces gravely, as if he’s delivering the Gettysburg Address, and John takes a moment to try to absorb what he’s just heard

Can I get links on the last two?

Than you for the recs. *Cookie for u*

Pre-series (Stanford years) John and Dean:
http://www.fanfiction.net/s/3677476/1/Dirty_Tactics
Possibly my favorite John fic, and the interaction is so well-written you can *see* it.

thnx for the recs.

Everything in dean_adam is great. I read nearly all the posts in it and they were lovely! Sadly, it's not all that active. :(

Thanks, I was almost going to post again for Dean/Adam.