I'm not really up on time travel fic but for cross-overs, start with the SPN crossover community on LJ here (http://sn-crossovers.livejournal.com). Most of my favourite cross-overs are linked from there. If you are interested in Buffy or Angel crossovers with SPN, then Twisting the Hellmouth (http://www.tthfanfic.org/) is the place to look.

One of my favourite 'Dean doesn't get Sam from Stanford' AUs is the epic The Amazing incredible Adventures of Freakboy and Dyke Girl (http://archiveofourown.org/works/695404/chapters/1279159). I was upset when my previous bookmarks didn't work, but the author is in the process of transferring all her fic to AO3.

Thank you - I'll check these out! Keep' em coming!!!

Hey. I thought wolverines, wendigos etc wasn't finished? If she's finished it I would love the link - please?

It isn't finished yet, I'm afraid - it's up to ch 106 right now at fanfic.net. I'm eagerly awaiting the next installment, lol!

it's finished.

X-Men crossovers

http://nekare.livejournal.com/404440.htmlv (gen)
http://web.archive.org/web/20080610151622/http://www26.brinkster.com/scynneh/proving%20otherwise.html (gen)
http://slashfest.livejournal.com/155017.html#cutid1 (Dean/Gambit)
http://hunters-retreat.livejournal.com/244811.html?style=mine (Dean/Eliot/Logan spn/xmen/leverage)
http://archiveofourown.org/works/640935 (Dean/Gambit)
http://archiveofourown.org/works/587289/chapters/1055720 (Dean/Cas, Sam/Xavier, also has heroes characters)
http://archiveofourown.org/works/433915/chapters/736155 (gen)
http://archiveofourown.org/works/331305 (Dean/Remy)
http://archiveofourown.org/works/364153 (leverage/spn/xmen, Eliot/Dean/Remy)
http://archiveofourown.org/works/58202 (Dean/Sam/Rogue)
http://archiveofourown.org/works/82424 (Dean/Logan)

And there's the x-men tag at the spn crossovers bigbang comm - http://sncross-bigbang.livejournal.com/tag/supernatural%2Fx%20men

Thanks so much! You're a star!

I don't think these x-men crossovers have gotten a mention yet (though they might be on one of those communities):

Devil and Flames (http://deep-salt-water.livejournal.com/341667.html)
Summary: The Winchesters cross paths with a mutant girl known only as Rogue, and things start to get a little complicated.
Word Count: Didn't see one for the whole story but it is Multi-chaptered

If it's not happy, at least it's not sad either (http://archiveofourown.org/works/211213)
Summary: Sam starts wearing gloves when he’s around twelve. From then on, the Winchesters' lives can never be the same anymore.
Word Count: 9,000

Shake It Off (http://rbmi-fan.livejournal.com/1046.html)
Summary: Dean's a mutant, and that's a problem.
Word Count: 4,000

These next to aren't finished, but I'm hoping...
Awakening (http://anansispidergod.livejournal.com/1032.html#cutid1)
Summary: Author didn't write one, but so far it's about the boys getting powers

Not Alone (http://archiveofourown.org/works/323970/chapters/521776)
Summary: Castiel Novak hides a terrible secret about a frightening ability and as far as he's concerned, no one will ever have to know. Which works pretty well up until he sprouts wings in his fourth period class. Soon after, he finds himself at Xavier's School for Gifted Youngsters where he discovers he's not the only freak with a secret.

I've also got some other crossovers on my delicious (https://delicious.com/allhailaugustus/crossover) and there have been some pretty good general crossover recs in some old posts on this community like this post (http://spnstoryfinders.livejournal.com/1842307.html#comments).

For your other request, these might work:
Looking through Windows (http://faithburke.livejournal.com/57491.html#cutid1)
Summary: Sam Winchester had turned his back on his father's world, but now something has taken his son and he'll do anything to get him back. Including calling his brother.
Wordcount: 22000

Sibling Metamorphosis (http://faithburke.livejournal.com/73139.html)
Summary:Its Halloween night, 2005, and Sam discovers an unexpected visitor in his apartment. Sequel to Parental Evolution.
Word Count: 14,000

I know there are some others, I just can't think of them right now. I know there's a oneshot where Dean writes romance novels, which will never stop being head cannon for me.

The bigbang quickreaver and I co-wrote last year, Burdens, Doublefold (http://blood-and-pie.livejournal.com/12194.html) is about Dean not getting Sam from Stanford. Dean hunts with John for a while, and the story follows both Dean and Sam on their journeys until they're reunited at the end. Dean spends time at the Roadhouse with Ellen, Jo and Ash as well, and Sam travels with Brady seeking revenge for Jessica's death on his own.

Thanks so much - I'll give it a read!