The opening song to Chuck, Cake's "Short Skirt/Long Jacket", a song that only gets more epic once you've heard the whole thing.
In "Chuck vs. Tom Sawyer," Rush's "Tom Sawyer" is revealed to be the underlying code in Missile Commandwhich allows Chuck to reach a missile code and prevent World War III. The song plays over a sequence of Sarah beating up a mook, Casey preparing to deploy the Air Force, and Chuck winning the game, creating an epic, uniquely nerdy climax.
Twisted Sister's "We're not gonna take it anymore" when the employees rampage through the Buy More and Team Chuck is invading Fulcrum in "Chuck vs The First Kill." Doesn't get more awesome than that.
Halfway through the season 2 finale, "Chuck vs. The Ring", a firefight of epic proportions between Team Chuck and Evil!Chevy Chase is only make more awesome by the musical accompanyment, a live performance of "Mr. Roboto" by Jeffster. Just... yeah. Just watch.
The use of Crooked Fingers' "Luisa's Bones" in "Chuck vs. the Dream Job" perfectly underscores the scene's mix of mystery, intensity, and sheer badassery as Chuck figures out Roarke's plans and resolves to go after him on his own.
In "Chuck vs. the Suburbs," Chuck's introduction to the fake "American dream" life the CIA has created for his and Sarah's latest cover is accompanied by Talking Heads' "Once In A Lifetime." The music fades out shortly after "And you may say to yourself/'This is not my beautiful house/This is not my beautiful wife!'"
Any time Frightened Rabbit is used (which is a few times, Josh Schwartz is clearly a fan), particularly "Backwards Walk" when Chuck leaves Sarah in Prague in the season 3 opener, and probably the best example (in early-ish season 2): "Keep Yourself Warm", when Chuck is with Jill as Casey and Sarah find out who she really is. Truly awesome music used absolutely perfectly.
Any song performed by Jeffster has to count as this as well as a Funny Moment.
The last three minutes of "Chuck Versus the Push Mix", in which Ellie gives birth to her baby, Alex and Casey reassure each other that they are both in each other's lives to stay, and Chuck, having defeated Volkoff and put his family back together, finally proposes to Sarah, is such a joyful scene for every single one of them, and that sense of jubilation is perfectly underscored by the use of "Young Blood" by The Naked and Famous.
The team race to track down the poisoner who has the antidote to the truth serum which is slowly killing them to the tune of Britney Spears's "Toxic" in "Chuck Versus The Truth".