There's a whole list of wonderful MU fics - it's a fun place to play after all.
I wrote my TnT fic, "A Mirror Cracked" with idea that I'd resolve the whole mind meld issue, and while it took me awhile, I managed to do it and decided T'Pol was just doing her job and didn't mean to do any harm. Tucker sided with Archer, so he opened himself to action. Sure, it took me 11 chapters for them to resolve this - but it was fun.
Misplaced is currently revamping her "Reflections of Another Universe". Pdsldl has got "Double Vision" going on.
And Lady Rainbow has her "A Pact With Mephisto" running.
Obviously, the MU is a fertile creative ground. I tend to like my MU fics that take the approach that the show did: These are not the evil versions of the RU characters, but what they would have become had they grown up/had to operate in the harsh world that is the MU. I had my main characters (TnT) really want to be like their RU counterparts, but they also knew they couldn't. They had to reach for the better versions of themselves that were available in their own universe.

