If you mean just not your standard Pilot starting point, here are a couple of my favs:
When Larry Met Charlie by Wendy Richards
Is one of my all time favorite alt beginning stories (and LnC fics in general). It parallels the Pilot's plot but with a few very important variations.
Meet me in Kansas City by Chris Mulder
Is also fabulous. It's an entirely different initial circumstance as well.
There are many other very good ones out there, but I'll limit myself to just these two =)
