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