'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.