Here are a few of my favorite long stories, sorry most of these are not humorous. All of the stories I have in my humor file are less than 10k in length. These are all Dean/Cas.

Long and Lonesome Highway by Sorka42 http://archiveofourown.org/series/14143

Metaphysical Gravity by zoemathemata. http://zoemathemata.livejournal.com/10445.html

There's Only One Sure Thing That I Know by blinkiesays. http://blinkiesays.livejournal.com/144440.html. This one has some humor.

The Long Road Back by Nicole. http://bleeding-muse.livejournal.com/78176.html.

Convenient Husbands by Annie D. http://archiveofourown.org/works/432705. They have this tagged as a romantic comedy.

Ghosts of Future Past by etrix. http://archiveofourown.org/works/512891/chapters/904602. Most of this author's stories are on the long side, so you might want to look through them, although they usually are pretty angsty.

A Subtle Touch of Grace by bluetoastfics. http://bluetoastfics.livejournal.com/28925.html. A good story, but a definite tearjerker.