Avengers / Thor / Iron Man 3 / Captain America
Like Green Lantern and Astro Boy, Marvel’s pile of Phase One prequels are good examples of comics that are all about movie continuity rather than the established canon from the page. The eight-part Captain America: First Vengeance, for example, goes the one-issue-per-character route, setting up Rogers' and Bucky's childhood friendship. The two-part Thor prequel, meanwhile, gives us some youthful Thor/Loki rivalry, and a mission to Svartalfheim to rescue Fandral.
The Avengers Prelude – subtitled Fury’s Big Week – is an amusing eight-part runaround centred on Nick Fury and Agent Coulson, recapping what happened in the previous Phase One movies, and giving Hawkeye a bit more attention than Avengers Assemble really bothered with. The overarching plot has General Thunderbolt Ross (seen in the Hulk movies in various guises) trying to oust and replace Fury at S.H.I.E.L.D.
As Phase Two begins, we so far have two comics filling gaps after Avengers Assemble. The two-part Iron Man 3 Prelude explains War Machine’s Avengers absence, and the Thor: The Dark World Prelude (two instalments) tells us what the Asgardian was up to during Assemble’s first twenty minutes. Surprisingly, the answer is neither "conditioning his lovely hair" or "working those biceps".