Theme Music Withholding

You worried they would pull some Theme Music Abandonment, it made you mad. Your resigned to the fact that They Changed It, Now It Sucks, but them the theme comes roaring back at just the right moment. Sometimes it's just a Fan Wank, but usually it's withheld to create a massive Crowning Moment of Awesome at just the right moment. The practice of holding back some familiar theme music is often done in reboots or somewhat distant sequels.The familiar theme music once commonplace is played now only at the end.

Anime

 * Sailor Moon: Sailor Stars replaces the previous (and only other) opening theme, "Moonlight Densetsu", with "Sailor Star Song". "Moonlight Densetsu" makes its first appearance since Super S and only appearance in Sailor Stars at the end of the final episode. Combined with Usagi's monologue it serves as bookends back to the very first season as well.

Film

 * Terminator 3 Rise of the Machines: Brad Fidel's theme is heard only in the credits.
 * Casino Royale: The James Bond theme plays in full over the ending and credits.
 * Star Trek: Alexander Courage's theme plays in full over the final sequence and in the ending credits, and it's awesome.
 * Sukiyaki Western Django: a cover of Franco Migliacci's Django theme appears in the final scene.
 * Halloween, the sequel to the remake: The theme is heard only in the end.
 * The Spider-Man film used the old animated TV show theme song in the end credits.
 * The 2011 film adaptation of The Green Hornet only uses the classic theme in its final scenes.
 * The final Harry Potter takes its time in introducing the iconic theme.
 * Iron Man is arguably an example. While there is no 'definitive' Iron Man theme, EVERYBODY was waiting for the Black Sabbath song. EVERYBODY had to wait until the last 10 seconds of the movie (and credits).
 * The 2005 The Hitchhikers Guide to The Galaxy movie swapped out the traditional "Journey of the Sorcerer" with a new, original song based around the dolphins leaving Earth for the credits ("So Long and Thanks for All the Fish"). "Sorcerer" is used as fanfare to lead into the narrator introducing the Guide itself.

Live Action TV

 * Star Trek: Enterprise: The Courage/Goldsmith theme is used in the ending sequence of the final episode.
 * Battlestar Galactica: The original series theme is used sparingly. Once in a blink-and-you-miss-it cameo during the miniseries, once as a full-blown orchestral arrangement in the episode "Final Cut" (that was arranged with the input of original series composer Stu Phillips), once during the flashback battle in the film Razor (a purely Bear McCreary arrangement), and one last time during the final scene featuring Galactica.
 * Law and Order LA: The theme is not used till after the Retool.
 * Smallville: John Williams' iconic Superman March plays in full during the last moments of the final episode pleasing the Unpleasable Fanbase and saving the world!

Video Games

 * Metal Gear Solid 3: Snake Eater: An acoustic version of the main theme is played in the last few minutes of the end credits
 * The Legend of Zelda: Twilight Princess
 * Wind Waker drops Zelda's Lullaby during the credits -- on top of the Wind Waker title theme. What makes it even cooler is the two themes are in 3/4 and 9/8 respectively, so you get this awesome polyrhythmic effect.
 * Final Fantasy V, VI, and VII all save the eponymous theme of the series until after the final boss.
 * Castlevania: Lament of Innocence only features the classic theme "Vampire Killer" during the end credits.
 * Fire Emblem: Path of Radiance has the iconic Fire Emblem Main Theme only featured at the final battle results, after the end credits.
 * Deus Ex Human Revolution waits until after the end credits to play the classic title screen theme from the first two games.