'We travel without seatbelts on' by victoria_p - instead of joining the FBI, Veronica Mars is recruited by SHIELD and ends up going back to Neptune after the truth is revealed about HYDRA. She's not the only one who ends up there. Gen.
'Half a Minute and Thirty Seconds' by mrasaki - a nicely-written crossover (if you can have such a thing) between the movie universe and the storyline of Matt Fraction's Hawkeye comic, tying together the storylines of both very neatly. Clint/Phil.
'If We Never Got This Second Chance' by Pookaseraph - when Tony and Steve’s son from the future, Jake Jensen, arrives at Avenger’s Tower, the two of them are forced to confront some hard truths: Tony that he might not actually become a horrible father, and Steve that he might not be able to set aside his discomfort with sharing a child with another man. Steve/Tony.
'I Lie, I Cheat, I Steal (and I Just Don't Get Any Respect)' by fiercelydreamed - a nice crossover between two of my current favourite shows, where Nate decides that what they really need for their next con is a particular con artist, one who's currently working with the FBI. Various pairings implied.