The rapper Fabolous had a hit song "Breathe" several years ago that contained a sample from a Supertramp song. The track leaked and became HUGE before they cleared the sample, so when it came time to negotiate Supertramp had all the leverage. Supposedly they got $100,000 plus almost all royalties, so Fabolous didn't make any money off the single. (Though of course he made tons on album sales).
EDIT: Just because you're supposed to clear samples doesn't mean people always do. If a sample is obscure enough or sufficiently altered, artists may try to get away with it hoping that no one will notice -- apparently that's the case with Daft Punk. I think Timbaland has gotten into trouble sampling foreign artists without permission ("Big Pimpin'", maybe), and the source of the sample in Nas's "Nas is Like" went unknown for around a decade. See http://www.whosampled.com/sample/4061/Nas-Nas-Is-Like-John-V...