They lost to The Smashing Pumpkins "Tonight, Tonight" if I remember correctly.
EDIT - Yup. Damn they actually got shut out.
Video of the Year
The Smashing Pumpkins "Tonight, Tonight" - WINNER
Bone Thugs-n-Harmony "Tha Crossroads"
Foo Fighters "Big Me"
Alanis Morissette "Ironic"
Best Group Video
Foo Fighters "Big Me" - WINNER
Bone Thugs-n-Harmony "Tha Crossroads"
The Fugees "Killing Me Softly"
Hootie & the Blowfish "Only Wanna Be with You"
Best Rap Video
Coolio (featuring L.V.) "Gangsta's Paradise" - WINNER
2Pac (featuring Dr. Dre and Roger Troutman) "California Love"
Bone Thugs-n-Harmony "Tha Crossroads"
LL Cool J "Doin It"
Best Special Effects in a Video
The Smashing Pumpkins "Tonight, Tonight" (Special Effects: Chris Staves) - WINNER
The Beatles "Free as a Bird" (Special Effects: Johnny Senered, Kristen Johnson and Ben Gibbs)
Bone Thugs-n-Harmony "Tha Crossroads" (Special Effects: Cameron Noble)
Green Day "Walking Contradiction" (Special Effects: Jefferson Wagner and Brian Boles)
Viewer's Choice
Bush "Glycerine" - WINNER
Bone Thugs-n-Harmony "Tha Crossroads"
Coolio (featuring L.V.) "Gangsta's Paradise"
Metallica "Until It Sleeps"
Alanis Morissette "Ironic"
The Smashing Pumpkins "Tonight, Tonight"