Here are the sounds that I think are significant:
BARMUSIC.VOC The E1L2 bar music with more bass than in the final release.
RECORG.VOC Police siren, from beta E1L2.
SEEN01.VOC "Already seen this one." (referring to the movie in E1L1)
THINK06.VOC "Hmm, I don't think so!"
The rest of these vary from the final versions in volume and sound quality.
Additionally, the DUKE.RTS file (used for Remote Ridicule audio taunts) contains one removed sound:
DUNG01.VOC "Way to go, dung brains."
It was later replaced with DSCREM04.VOC, the death scream that plays when falling from a great height.