My favorite Ghost!Dean story is Somewhere A Clock Is Ticking by parenthetical
Summary: When Ben goes missing, Dean has to help, even if it means going in without Sam. By the time he stops to consider the consequences, it's already too late, and Sam's skating dangerously close to the edge in his determination to fix things. http://archiveofourown.org/works/1182/chapters/1411

Haha I've seen that fic around and never realized it was a ghost! Dean story. Thanks :D

Huh... maybe I should have warned for spoilers then? :)

Riding Shotgun (http://bythedamned.livejournal.com/10436.html) is an excellent ghost!Dean fic though it's ending probably isn't the happy you sound like you're looking for, though it is cheerful. It's gen, starting off in s4.
Summary: "Sam doesn’t know how he can say his brother is dead when there’s still someone on this earth who looks at him like that." For the Winchesters, death is never the end.

I'll give it a try. Thanks

Actually, coming back to this comment reminded me of another fic: Scheherazade of the Super Eight (http://pyrebi.livejournal.com/38205.html). It's gen s6 with Dean and Cas as the main players. It's good and Dean being dead is kinda central to the story, though I'd kinda forgotten about the dead part myself, lol.
Summary: Dean doesn't know why angels keep recruiting him for impossible tasks. But they do, and now he's apparently the last chance heaven has--not only against Raphael, but against a dangerously unhinged Castiel. Oh yeah, and he has to do it all from the confines of a 10'x16' motel room that doesn't even exist.

There's a ghost!Jensen fic called Heaven's Just a Sin Away by jeyhawk (http://jeyhawk-fic.livejournal.com/46023.html) which fits the bill, but it's a J2 fic and I'm not sure if you're up for that sort of thing? It's worth a read, though :)

J2 is great! Thanks

Here's some Spirit!Dean fics from In My Time If Dying

Spirit (http://www.fanfiction.net/s/3412300/1/Spirit) by Ciya (http://www.fanfiction.net/u/721897/Ciya)
Summary: AU What could have happened in the epi 'In My Time Of Dying' if Sam was the only one who could see Dean.

ALl For One, One For Both Bring A Spirit Sucks (http://www.fanfiction.net/s/4144082/1/All_For_One_One_For_Both_Being_a_Spirit_Sucks) by authoressnebula
Summary: Season 2x01: In My Time Of Dying: Sam only missed John by a fraction of a moment. So...what if he hadn't missed him? What if he'd followed John down? An AU, what-if for the episode.

ghost!Dean

I Touch the Place Where I’d Find Your Face by lotsayaoi
Summary: AU of season 2, starting with 2.01 In My Time of Dying. When Tessa asks Dean whether he’s ready to move on or if he wants to stay, Dean does what he must to protect his brother. Dean follows Sam as he hunts, taking care of him and learning how to be a spirit, and they both learn just how strong love that crosses the veil can be. And how weak.
http://lotsayaoi.livejournal.com/7693.html

You Take It With You by lazy_daze
Summary: Sam saves the world, and he brings Dean back from a month in Hell, but that's when things start to get complicated. Dean's cheated death before, but this time, it's different – Dean's spirit is unable to re-enter his body. Can Sam and Bobby work out how to reunite Dean's body and spirit? And how will Dean cope if they can't? From hunts in the Chicago lakes to visits to the Grand Canyon, with dreams, handjobs and hookers along the way, Sam and Dean ride it out and learn all over again how to live this life and live it together.
http://lazy-daze.livejournal.com/483411.html#cutid1

The Gospel of Dean by smalltrolven
Summary: Dean dies, Sam drives and gets a surprise ghostly passenger who loves to talk and ask questions. The King of Hell pays back a debt and Heaven’s reward is finally granted.
http://smalltrolven.livejournal.com/2772.html




ghost!Jensen

So Close No Matter How Far by TempestQuill/Cassie
Summary: Five amazing years working with the guy who's become his best friend. Now the time has come to move on, but Jensen Ackles is learning that there's always something to be said about goodbyes, and just how final they can be, especially when Jared Padalecki isn't ready to hear it...
http://tempestquill.livejournal.com/53709.html



edited because I realized this one's a different type of ghost story, but one that I think you might enjoy...


The Ghost by hunters_retreat
Summary: Thirty years ago, humanity was changed. The magic they scoffed at as nothing more than fairy tales and children's illusions was real and the barrier that separated them from that and the world of the fae came crashing down. In the wake of that phenomena, new government agencies were created to deal with the problems of magic in the modern world. Humans relied on the men and women of the DMI to protect them from the abuses of magic. But when Agent Padalecki finds himself in the middle of a murder investigation with a civilian on his scene, he realizes it's not just any civilian. The intruder is the Ghost, a fae that even the high Seelie court fear. Faced with a murder investigation and a possible connection to a string of killings, Agent Padalecki must find a way to work with the Ghost to stop a killer before he can do the unthinkable; start a war between humanity and fae.
http://hunters-retreat.livejournal.com/425954.html?view=3174626

Edited 2012-08-12 05:41 am (UTC)

Dean/Tessa with (sort of) ghost!Dean:
Rustling in the Dark (http://lavendergaia.livejournal.com/323800.html)

This is really long, AU, and Wincesty, but if all that works for you this is a beautiful story. How exactly it's ghost!Dean is explained in the author's note...
http://ht-murray.dreamwidth.org/tag/something+gold (http://ht-murray.dreamwidth.org/tag/something+gold) the internal links to the parts no longer work, but it is all here.

Edited 2012-08-12 02:40 pm (UTC)

Jensen's a ghost for most of this, but not all of it, but it does have a happy ending - hope J2 is okay: Tragedy of Life by lizzywinks http://lizzywinks.livejournal.com/14001.html

Late to the party, but here is my contribution of ghost!dean fics on Delicious.

https://delicious.com/jpgr/theme%3A%20ghost!dean