The Blue Öyster Cult classic "(Don't Fear) The Reaper" playing over the beginning of "Turn, Turn, Turn". It proves to be what Agent Garrett was listening to on his plane's sound system at the time. Just because you're a HYDRA agent doesn't mean you can't have great taste in music. On top of that, the real-life USAF operates the MQ-9 "Reaper" armed UAV.
Audrey Nathan's (the cellist) piece in "The Only Light In the Darkness". For the filming, actress Amy Acker (not a cellist in Real Life) just mimed playing the cello. McCreary created an entirely original cello composition based on Acker's finger and bow movements that sounds like a beautiful classical piece.
The last scene of "The Writing of the Wall" of Ward shaving and Skye checking the phone is awesomely set to "Who is He (And What Is He to You)" by Bill Withers.
The musical cue at the end of "What They Become", where Skye emerges from the Terrigen Mist and cements her role as the MCU incarnation of Daisy Johnson/Quake. Which sees a reprise at the end of Season 2 as Daisy battles her mother to save herself and all non-Inhumans and a further Dark Reprise in "The Team" when Daisy reveals herself to have been infected by Hive and proceeds to devastate the SHIELD base with her sonic powers.
The Leitmotif for 'Tahiti' and anything relating to it is an incredibly unnerving One-Woman Wail that often heralds something very creepy.
The nightmarish theme from "S.O.S." that plays when Cal becomes Mr. Hyde.
Another McCreary creation,"Crossing into Darkness", the epic piece that ends "Maveth" is pretty awesome in his own right. It makes a fantastic return in "The Real Deal" as the music which plays when Mike Peterson lands a Quinjet in the Lighthouse carrying agents that Deke was able to contact. The song plays during what is effectively the rebirth of S.H.I.E.L.D.
The tune that plays during 'Parting Shot' when the team says goodbye to Bobbi and Hunter. Made doubly awesome because so much of the scene is only the music, no words were said. The music alone drove home the finality of the goodbye.
The theme that plays whenever Ghost Rider appears is ominous and awesome at the same. When it plays during the Rider's first appearance, it lets you know straight away that the characters and audience are not dealing with a natural, scientifically grounded force, but a supernatural demon that no one is prepared for. From then on, every other time it's played, you know whoever's in his target-sight is completely and utterly screwed. "It's time to pay for your sins" indeed.
The music from Life-Model Decoy Coulson and May's conversation in the climax of "Self Control", which gradually grows from sad and tragic to triumphant and incorporates the show's main theme in the most moving way possible.
The score in the climax of "No Regrets", which serves as a moving and fittingly emotional goodbye to Jeffrey Mace.
Sinara's theme from Season 5. It is so strange and overworldly that it immediately conveys not just the danger itself, but the absolutely alien aspect of it.
The score during the end of "Orientation: Part One," when the agents try to figure out where they are after being sent through a Monolith at the beginning of the episode. Daisy, Mack, Yo-Yo, Coulson, May, and Simmons all gradually begin to realize that something is very wrong about their location, climaxing when Coulson realizes that the Monolith didn't send them through space as May points out a wrecked half of a schoolbus floating out in front of a tiny sliver of a particular blue-and-green planet.
The official Season 6 trailer features a spectacular cover of "In the End" by 2WEI that's fittingly appropriate for both the solemn melancholy and dimension-hopping madness that this upcoming season looks to deliver.
The Season 6 finale gives Sarge a rather sinister Leitmotif during the final battle between him and the agents in the temple, which perfectly captures the feeling of how doomed the agents are with May effectively dead, Yo-Yo possessed by a Shrike and Sarge completely immune to both Daisy's quake blasts and the Shrike-killing bullets as well as the interdimensional reality-warping weirdness of this season.
Season 7's time travel shenanigans have given us some wonderfully period-appropriate music, especially a 70's-tacular version of the main theme from episode 5.