Here are a few, all gen and heavy on the crossovers:

Red (http://www.fanfiction.net/s/3169840/1/Red) by BigPink
Summary: Something evil is killing treeplanters in the forests of the Pacific Northwest, possibly the same predator that Dean narrowly escaped years before. How Grimm will things get before the brothers figure it out?

Cross Creek (http://zoemathemata.livejournal.com/18183.html) by zoemathemata
Summary: The Winchesters check in at Cross Creek Hotel to purge its ghostly guests. It is widely known that the hotel is haunted and every year thrill-seeking tourists check in to experience the supernatural, but as far as the Winchesters are concerned, there’s no such thing as a happy haunted hotel.

A Loaded God Complex (http://spn-summergen.livejournal.com/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).

Harvester of Eyes (http://spn-boc.livejournal.com/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. You don't need to be familiar with Sandman!

Howl (http://archiveofourown.org/works/165795?) by seraphim_grace
Batman adopts the wee!chesters

Pyromaniac (http://tigriswolf.livejournal.com/223718.html) by tigriswolf
The first time Dean controlled fire he was thirty-three, way too old to develop a power. And fire? Not cool. Not cool at all. Crossover with The X-Men.

Wolverines, Wendigos and Winchesters (http://www.fanfiction.net/s/5155714/1/Wolverines_Wendigos_and_Winchesters) by SciFiNutTX
SN pre-series / post X-Men Origins: Wolverine - Dean meets Wolverine during a solo hunt, which leads to friendship and a new job.

The Art of Survival (http://www.tthfanfic.org/Story-11900/gbholderness+The+Art+of+Survival.htm) by gbholderness
Albus Dumbledore hires John Winchester and his sons to teach Defense Against the Dark Arts. Supernatural/Harry Potter crossover.

The Boy Who Saw Death (http://lexicale.livejournal.com/35302.html) by lexicale
Summary: Sam looked forward to getting his letter for years. He couldn't wait to be where Dean was, doing what Dean did, but when he finally turns eleven, things don't work out quite how he had expected.

Mended (http://www.fanfiction.net/s/5170979/1/Mended) by PaBurke
Summary: It was always Sammy bringing home broken animals needing fixing, but Dean had the same soft heart. It just revealed itself in different ways.

Thank you! So much awesomeness- and he'll adore the X-men crossovers!