IFC has this up-to-date explanation of the overuse of just about every version of Leonard Cohen's "Hallelujah" to score everything from The West Wing to Watchmen.
But there are other offenders as well. I recall a moment in the late '90s when it appeared that just about everything was accompanied by Kate Bush singing "This Woman's Work." That whole business started here, in 1988, in a surprisingly sweet montage from the John Hughes film She's Having A Baby, for which the song was apparently written.
What would you nominate for the It's A Pretty Song, But Enough Already Hall Of Fame?